Jean-Philip Piquemal

CV de Jean-Philip Piquemal
226
Documents
Affiliation actuelle
  • Sorbonne Université (SU)
Contact

Présentation

**Jean-Philip Piquemal Sorbonne Université (SU), Laboratoire de Chimie Théorique, UMR 7616 CNRS, Tour 12-13, 4 place Jussieu, 75252 Paris Cedex, France. Tel:(+33) 144272504 ; FAX: (+33)144274117 ; E-mail : jean-philip.piquemal (at) sorbonne-universite.fr ; Homepage: http://piquemalresearch.com; Bluesky: @jppiquem.bsky.social(personnel); @piquemalgroup.bsky.social (équipe de recherche) X: @jppiquem (personnel); @piquemalgroup (équipe de recherche) Mastodon: @jppiquem(personnel) LinkedIn: @jppiquem

Biography Jean-Philip Piquemal est chimiste théoricien, professeur de classe exceptionnelle à Sorbonne Université (SU) et directeur du Laboratoire de Chimie Théorique (SU/CNRS, UMR7616). Ses recherches portent sur le développement de techniques de simulation moléculaire de nouvelle génération, fondées sur la chimie théorique et les mathématiques appliquées. Il est Principal Investigator du projet ERC (European Research Council Synergy) Synergy Extreme-Scale Mathematics-based Computational Chemistry (EMC2). Ses travaux mettent particulièrement l'accent sur la conception et l'implémentation de champs de force avancés et de potentiels interatomiques issus du machine learning (MLIP) dans les architectures matérielles du HPC à l'informatique quantique. Il utilise ces techniques pour résoudre des problèmes de chimie quantique à grande échelle en biologie et en science des matériaux pour des applications biomédicales ou orientées énergie. Jean-Philip Piquemal est directeur scientifique (CSO) et co-fondateur de Qubit Pharmaceuticals (2025-présent), et Guest Faculty à Argonne National Laboratory (2025-présent).

Recherche

  • Chimie quantique;
  • Simulation moléculaire;
  • Sciences du médicament;
  • Informatique incluant High Performance Computing, Quantum Computing et Machine Learning.

Situation actuelle

Liste de publications mise à jour et Bibliométrie : Visitez mon profil Google scholar ou visitez ma page web : http://piquemalresearch.com/publications/

Développement logiciel Développement du logiciel Tinker-HP: dynamique moléculaire (https://tinker-hp.org).

Situation professionnelle

  • 2025-présent: Directeur-adjoint de l'initiative I-DREAM (Nouvelles Frontières de la Réactivité Moléculaire), Alliance Sorbonne Université.
  • 2023-présent : Professeur de classe exceptionnelle (PREX2), CNU section 31, SU.
  • 2020-présent : Membre du comité scientifique de PRACE (Partnership for Advanced Computing in Europe).
  • 2020-présent : Co-fondateur (2020) et directeur scientifique (CSO) de Qubit Pharmaceuticals
  • 2019-présent : Directeur du Laboratoire de Chimie Théorique (LCT), UFR de Chimie, SU & CNRS
  • 2019-présent : chef d'équipe, Extreme-scale Mathematically-based Computational Chemistry (EMC2), LCT, SU/CNRS.
  • 2019-présent : PI du projet ERC Synergy EMC2 (2019-2025)
  • 2019-2023 : Professeur de classe exceptionnelle (PREX1), CNU section 31, SU.
  • 2021 : President du jury (junior) de l'Institut Universitaire de France
  • 2016-2021 : Membre junior de l'Institut Universitaire de France
  • 2016-2019 : Professeur (première classe, PR1), CNU section 31, SU.
  • 2012-2019 : chef d'équipe MC2, projet interdisciplinaire au sein de l'ISCD (Institute for Computations and data), SU.
  • 2012-2018 : Directeur de l'Institut Parisien de Chimie Physique et Théorique (IP2CT), FR 2622, SU & CNRS
  • 2012-2018 : chef d'équipe, axe de recherche du LCT: «From quantum interpretative techniques to multiscale modeling».
  • 2011-2016 : Professeur (seconde classe, PR2), UPMC.
  • 2009-2011 : Maître de Conférences - HDR, UPMC.
  • 2006-2009 : Maître de Conférences, UPMC.
  • 2004-2006 : chercheur postdoctoral (NIH Visiting Fellow) au NIEHS, Research Triangle Park, NC, USA (groupe de Thomas Darden).

Formation

  • 2009 : Habilitation à Diriger des Recherches (HDR) en Chimie Théorique, UPMC.
  • 2004 : Thèse de doctorat en Chimie Théorique, Laboratoire de Chimie Théorique, UPMC. [Academic Genealogy]
  • 2001 : Diplôme d'Etude Approfondie (DEA) en Chimie Informatique et Théorique (DEA National CIT), UPMC.
  • 2000 : Maîtrise de Chimie (mention chimie physique), UPEC.

Affiliations: SU= Sorbonne Université; UPMC= Université Pierre et Marie Curie (Paris 6), now SU; NIEHS= National Institute of Environmental Health Sciences; UPEC = Université Paris-Est Créteil (Paris 12); CNRS= Centre National de la Recherche Scientifique

Enseignement Chimie théorique (chimie quantique et simulation moléculaire), chimie physique, machine learning, informatique et programmation.

Prix, bourses de recherche et distinctions

Industrie

Activités Editoriales

Sociétés scientifiques (membre)

  • Société Chimique de France (SFC)
  • Royal Society of Chemistry (RSC), FRSC (Fellow)
  • American Chemical Society (ACS)
  • Biophysical Society
  • Association for Computing Machinery (ACM)
  • Sigma Xi
  • International Society of Quantum Biology and Pharmacology (ISQBP): Councilor 2024-2028

Domaines de recherche

Chimie théorique et/ou physique

Publications

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Publications

The Convergence Frontier: Integrating Machine Learning and High Performance Quantum Computing for Next-Generation Drug Discovery

Narjes Ansari , César Feniou , Nicolaï Gouraud , Daniele Loco , Siwar Badreddine et al.

2026

Pré-publication, Document de travail hal-05558862v1

Experimental Realization of the Markov Chain Monte Carlo Algorithm on a Quantum Computer

Baptiste Claudon , Sergi Ramos-Calderer , Jean-Philip Piquemal

2026

Pré-publication, Document de travail hal-05544752v1

Logarithmic-depth quantum state preparation of polynomials

Baptiste Claudon , Alexis Lucas , Jean-Philip Piquemal , César Feniou , Julien Zylberman

2026

Pré-publication, Document de travail hal-05557135v1

Faster Molecular Dynamics with Neural Network Potentials via Distilled Multiple Time-Stepping and Non-Conservative Forces

Nicolaï Gouraud , Côme Cattin , Thomas Plé , Olivier Adjoua , Louis Lagardère et al.

2026

Pré-publication, Document de travail hal-05514212v1

A Foundation Model for Accurate Atomistic Simulations in Drug Design

Thomas Plé , Olivier Adjoua , Anouar Benali , Evgeny Posenitskiy , Corentin Villot et al.

2025

Pré-publication, Document de travail hal-05030352v1

Satellite Tobacco Mosaic Virus: Revealing Environmental Drivers of Capsid and Nucleocapsid Stability using High-Resolution Simulations

Marharyta Blazhynska , Olivier Adjoua , Zoe Vetter , Louis Lagardère , Jean-Philip Piquemal

2025

Pré-publication, Document de travail hal-04920167v1

Fast, systematic and robust relative binding free energies for simple and complex transformations : dual-LAO

Narjes Ansari , Félix Aviat , Jérôme Hénin , Jean-Philip Piquemal , Louis Lagardère

2025

Pré-publication, Document de travail hal-05428437v1

Practical protein-pocket hydration-site prediction for drug discovery on a quantum computer

Daniele Loco , Kisa Barkemeyer , Andre R. R. Carvalho , Jean-Philip Piquemal

2025

Pré-publication, Document de travail hal-05408143v1

An Optimal Framework for Constructing Lie-Algebra Generator Pools: Application to Variational Quantum Eigensolvers for Chemistry

Yaromir Viswanathan , Olivier Adjoua , César Feniou , Siwar Badreddine , Jean-Philip Piquemal

2025

Pré-publication, Document de travail hal-05389873v1

The Q-AMOEBA (CF) Polarizable Potential

Nastasia Mauger , Thomas Plé , Louis Lagardère , Simon Huppert , Jean-Philip Piquemal

2025

Pré-publication, Document de travail hal-04955664v1

From Water Networks to Binding Affinities: Resolving Solvation Dynamics for Accurate Protein-Ligand Predictions

Marharyta Blazhynska , Narjes Ansari , Louis Lagardère , Jean-Philip Piquemal

2025

Pré-publication, Document de travail hal-05320773v1

Quantum Circuits for the Metropolis-Hastings Algorithm

Baptiste Claudon , Pablo Rodenas-Ruiz , Jean-Philip Piquemal , Pierre Monmarché

2025

Pré-publication, Document de travail hal-05113563v1

A Foundation Model for Accurate Atomistic Simulations in Drug Design

Thomas Plé , Olivier Adjoua , Anouar Benali , Evgeny Posenitskiy , Corentin Villot et al.

2025

Pré-publication, Document de travail hal-05409397v1

A fully-polarizable KS-DFT/AMOEBA embedding scheme for plane wave basis sets through the MiMiC framework

Sonata Kvedaravičiūtė , Andrej Antalík , Olivier Adjoua , Thomas Plé , Louis Lagardère et al.

2025

Pré-publication, Document de travail hal-05409406v1

A fully-polarizable KS-DFT/AMOEBA embedding scheme for plane wave basis sets through the MiMiC framework

Sonata Kvedaravičiūtė , Andrej Antalík , Olivier Adjoua , Thomas Plé , Louis Lagardère et al.

2024

Pré-publication, Document de travail hal-04639146v1

Advancing Force Fields Parameterization: A Directed Graph Attention Networks Approach

G. Chen , T. Jaffrelot Inizan , T. Plé , L. Lagardère , Jean-Philip Piquemal et al.

2023

Pré-publication, Document de travail hal-04358188v1

ReaxFF Simulations of Self-Assembled Monolayers On Silver Surfaces and Nanocrystals

Adam Lahouari , Jean-Philip Piquemal , Johannes Richardi

2023

Pré-publication, Document de travail hal-04167690v1

Enforcing local DNA kinks by sequence-selective trisintercalating oligopeptides of a tricationic porphyrin. A polarizable Molecular Dynamics study.

Nohad Gresh , Krystel El Hage , Louis Lagardère , Frédérique Brégier , Jeremy Godard et al.

2023

Pré-publication, Document de travail hal-04172808v1

Accelerating Molecular Dynamics Simulations with Foundation Neural Network Models using Multiple Time-Step and Distillation

Côme Cattin , Thomas Plé , Olivier Adjoua , Nicolaï Gouraud , Louis Lagardère et al.

Journal of Physical Chemistry Letters, 2026, 17 (5), pp.1288-1295. ⟨10.1021/acs.jpclett.5c03720⟩

Article dans une revue hal-05304754v1

AMOEBA Polarizable Molecular Dynamics Simulations of Guanine Quadruplexes: from the c-Kit Proto-oncogene to HIV-1

Dina El Ahdab , Louis Lagardère , Zeina Hobaika , Théo Jaffrelot Inizan , Frédéric Célerse et al.

Journal of Chemical Information and Modeling, 2025, ⟨10.1101/2024.08.28.610081⟩

Article dans une revue hal-04680598v1

The need to implement FAIR principles in biomolecular simulations

Rommie Amaro , Johan Åqvist , Ivet Bahar , Federica Battistini , Adam Bellaiche et al.

Nature Methods, 2025, ⟨10.1038/s41592-025-02635-0⟩

Article dans une revue hal-04663318v1
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Polarizable models for selected Endocrine Disrupting Chemicals and their hosts

Anna Mazurek , Valentin Thirion , Lukasz Szeleszczuk , Jean-Philip Piquemal , Carine Clavaguera et al.

Journal of Computational Biophysics and Chemistry, 2025, ⟨10.1142/S273741652640003X⟩

Article dans une revue hal-05324665v2
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Targeting RNA with Small Molecules using State-of-the-Art Methods Provides Highly Predictive Affinities of Riboswitch Inhibitors

Narjes Ansari , Chengwen Liu , Florent Hedin , Jérôme Hénin , Jay W. Ponder et al.

Communications Biology, 2025, 8, pp.1405. ⟨10.1038/s42003-025-08809-y⟩

Article dans une revue hal-04742743v3

Greedy Gradient-free Adaptive Variational Quantum Algorithms on a Noisy Intermediate Scale Quantum Computer

César Feniou , Muhammad Hassan , Baptiste Claudon , Axel Courtat , Olivier Adjoua et al.

Scientific Reports, 2025, 15 (1), pp.18689. ⟨10.1038/s41598-025-99962-1⟩

Article dans une revue hal-04146321v1
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Targeting RNA with small molecules using state-of-the-art methods provides highly predictive affinities of riboswitch inhibitors

Narjes Ansari , Chengwen Liu , Florent Hédin , Jérôme Hénin , Jay W Ponder et al.

Communications Biology, 2025, 8 (1), pp.1405. ⟨10.1038/s42003-025-08809-y⟩

Article dans une revue hal-05498925v1
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VTX: Real-time high-performance molecular structure and dynamics visualization software

Maxime Maria , Simon Guionnière , Nicolas Dacquay , Valentin Guillaume , Vincent Larroque et al.

Bioinformatics, 2025, pp.btaf295. ⟨10.1093/bioinformatics/btaf295⟩

Article dans une revue hal-04917948v1
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Lambda-ABF-OPES: Faster Convergence with High Accuracy in Alchemical Free Energy Calculations

Narjes Ansari , Zhifeng Francis Jing , Antoine Gagelin , Florent Hédin , Félix Aviat et al.

Journal of Physical Chemistry Letters, 2025, 16 (19), pp.4626-4634. ⟨10.1021/acs.jpclett.5c00683⟩

Article dans une revue hal-05481035v1
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Non-Iterative Disentangled Unitary Coupled-Cluster based on Lie-algebraic structure

Mohammad Haidar , Olivier Adjoua , Siwar Badreddine , Alberto Peruzzo , Jean-Philip Piquemal

Quantum Science and Technology, 2025, 10, pp.025031. ⟨10.1088/2058-9565/adb3c5⟩

Article dans une revue hal-04678082v1
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High-resolution Molecular Dynamics Simulations of the Pyruvate Kinase Muscle Isoform 1 and 2 (PKM1/2)

Quentin Delobelle , Théo Jaffrelot Inizan , Olivier Adjoua , Louis Lagardère , Frédéric Célerse et al.

Chemistry - A European Journal, In press, ⟨10.1002/chem.202402534⟩

Article dans une revue hal-04377229v1

Lambda-ABF-OPES: Faster Convergence with High Accuracy in Alchemical Free Energy Calculations

Narjes Ansari , Zhifeng Francis Jing , Antoine Gagelin , Florent Hédin , Félix Aviat et al.

Journal of Physical Chemistry Letters, 2025, 16, pp.4626-4634. ⟨10.1021/acs.jpclett.5c00683⟩

Article dans une revue hal-04964833v1
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Histidine 73 methylation coordinates β-actin plasticity in response to key environmental factors

Adrien Schahl , Louis Lagardère , Brandon Walker , Pengyu Ren , Hugo Wioland et al.

Nature Communications, 2025, 16 (1), pp.2304. ⟨10.1038/s41467-025-57458-6⟩

Article dans une revue hal-03904639v1

Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model

Maxime Maria , Valentin Guillaume , Simon Guionnière , Nicolas Dacquay , Vincent Larroque et al.

Frontiers in Bioinformatics, 2025, 5, pp.1588661. ⟨10.3389/fbinf.2025.1588661⟩

Article dans une revue hal-04986917v1
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Velocity Jumps for Molecular Dynamics

Nicolaï Gouraud , Louis Lagardère , Olivier Adjoua , Thomas Plé , Pierre Monmarché et al.

Journal of Chemical Theory and Computation, 2025, 21 (6), pp.2854-2866. ⟨10.1021/acs.jctc.5c00023⟩

Article dans une revue hal-04852362v1

Lambda-ABF: Simplified, Accurate and Cost-effective Alchemical Free Energy Computations

Louis Lagardère , Lise Maurin , Olivier Adjoua , Krystel El Hage , Pierre Monmarché et al.

Journal of Chemical Theory and Computation, 2024, ⟨10.48550/arXiv.2307.08006⟩

Article dans une revue hal-04162777v1
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FeNNol: an Efficient and Flexible Library for Building Force-field-enhanced Neural Network Potentials

Thomas Plé , Olivier Adjoua , Louis Lagardère , Jean-Philip Piquemal

The Journal of Chemical Physics, 2024, 161 (4), pp.042502. ⟨10.1063/5.0217688⟩

Article dans une revue hal-04567115v1

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

F. Célerse , L. Lagardère , Y. Bouchibti , F. Nachon , L. Verdier et al.

ACS Catalysis, 2024, ⟨10.1021/acscatal.3c05560⟩

Article dans une revue hal-04290006v1
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Dynamic pre-structuration of lipid nanodomain-segregating remorin proteins

Zeren Xu , Adrien Schahl , Marie-Dominique Jolivet , Anthony Legrand , Axelle Grélard et al.

Communications Biology, 2024, 7 (1), pp.1620. ⟨10.1038/s42003-024-07330-y⟩

Article dans une revue hal-04821929v1
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Force Field X: A Computational Microscope to Study Genetic Variation and Organic Crystals Using Theory and Experiment

Rose A Gogal , Aaron J Nessler , Andrew C Thiel , Hernan V Bernabe , Rae A Corrigan Grove et al.

The Journal of Chemical Physics, 2024, 161 (1), ⟨10.1063/5.0214652⟩

Article dans une revue hal-04633495v1
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Shortcut to Chemically Accurate Quantum Computing via Density-based Basis-set Correction.

D. Traore , O. Adjoua , C. Feniou , I.-M. Lygatsika , Y. Maday et al.

Communications Chemistry, 2024, 7, pp.269. ⟨10.1038/s42004-024-01348-3⟩

Article dans une revue hal-04579665v1
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Leveraging Analog Quantum Computing with Neutral Atoms for Solvent Configuration Prediction in Drug Discovery

M. D’arcangelo , L.-P. Henry , L Henriet , D. Loco , Nicolaï Gouraud et al.

Physical Review Research, 2024, 6 (4), pp.043020. ⟨10.1103/PhysRevResearch.6.043020⟩

Article dans une revue hal-04214318v1
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Water-Glycan Interactions Drive the SARS-CoV-2 Spike Dynamics: Insights into Glycan-Gate Control and Camouflage Mechanism

M. Blazhynska , L. Lagardère , C. Liu , O. Adjoua , P. Ren et al.

Chemical Science, 2024, 15 (35), pp.14177-14187. ⟨10.1039/D4SC04364B⟩

Article dans une revue hal-04601083v1

Sparse Quantum State Preparation for Strongly Correlated Systems.

C. Feniou , O. Adjoua , B. Claudon , J. Zylberman , E. Giner et al.

Journal of Physical Chemistry Letters, 2024, 15 (11), pp.3197-3205. ⟨10.1021/acs.jpclett.3c03159⟩

Article dans une revue hal-04272837v1

Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-Polarizable Force Fields

Jorge Nochebuena , Jean-Philip Piquemal , Shubin Liu , G. Andrés Cisneros

Journal of Chemical Theory and Computation, 2023, ⟨10.1021/acs.jctc.3c00762⟩

Article dans une revue hal-04160556v1

Routine Molecular Dynamics Simulations Including Nuclear Quantum Effects: from Force Fields to Machine Learning Potentials

Thomas Plé , Nastasia Mauger , Olivier Adjoua , Théo Jaffrelot Inizan , Louis Lagardère et al.

Journal of Chemical Theory and Computation, 2023, ⟨10.1021/acs.jctc.2c01233⟩

Article dans une revue hal-03887583v1

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

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

Journal of Physical Chemistry Letters, 2023, pp.1609-1617. ⟨10.1021/acs.jpclett.2c03722⟩

Article dans une revue hal-03819436v1

Extension of the Trotterized Unitary Coupled Cluster to Triple Excitations

Mohammad Haidar , Marko Rančić , Yvon Maday , Jean-Philip Piquemal

Journal of Physical Chemistry A, 2023, ⟨10.1021/acs.jpca.3c01753⟩

Article dans une revue hal-03912869v1

ANKH: A Generalized O(N) Interpolated Ewald Strategy for Molecular Dynamics Simulations

Igor Chollet , Louis Lagardère , Jean-Philip Piquemal

Journal of Chemical Theory and Computation, 2023, ⟨10.1021/acs.jctc.3c00015⟩

Article dans une revue hal-03902427v1

QM / AMOEBA description of properties and dynamics of embedded molecules

Michele Nottoli , Mattia Bondanza , Patrizia Mazzeo , Lorenzo Cupellini , Carles Curutchet et al.

Wiley Interdisciplinary Reviews: Computational Molecular Science, 2023, ⟨10.1002/wcms.1674⟩

Article dans une revue hal-04122813v1
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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 , Jean-Philip Piquemal

Chemical Science, 2023, ⟨10.1039/D3SC02581K⟩

Article dans une revue hal-03917901v1

Smooth Particle Mesh Ewald-integrated stochastic Lanczos Many-body Dispersion algorithm

Pier Paolo Poier , Louis Lagardère , Jean-Philip Piquemal

The Journal of Chemical Physics, 2023, 159 (15), pp.154109. ⟨10.1063/5.0166476⟩

Article dans une revue hal-04153125v1
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Open Source Variational Quantum Eigensolver Extension of the Quantum Learning Machine (QLM) for Quantum Chemistry

Mohammad Haidar , Marko J. Rančić , Thomas Ayral , Yvon Maday , Jean-Philip Piquemal

Wiley Interdisciplinary Reviews: Computational Molecular Science, 2023, 13 (5), pp.e1664. ⟨10.1002/wcms.1664⟩

Article dans une revue hal-03698549v1
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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 et al.

Chemical Science, 2023, 14 (5438-5452), ⟨10.1039/D2SC04815A⟩

Article dans une revue hal-03738403v1
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Overlap-ADAPT-VQE: Practical Quantum Chemistry on Quantum Computers via Overlap-Guided Compact Ansätze

César Feniou , Muhammad Hassan , Diata Traoré , Emmanuel Giner , Yvon Maday et al.

Communications Physics, 2023, 6 (1), pp.192. ⟨10.1038/s42005-023-01312-y⟩

Article dans une revue hal-03955111v1

Calculating the ground state energy of benzene under spatial deformations with noisy quantum computing

Wassil Sennane , Jean-Philip Piquemal , Marko J. Rančić

Physical Review A, 2023, 107, pp.012416. ⟨10.1103/PhysRevA.107.012416⟩

Article dans une revue hal-03608627v1

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

Krystel El Hage , Giovanni Ribaudo , Louis Lagardère , Alberto Ongaro , Philippe H. Kahn et al.

Journal of Chemical Information and Modeling, 2022, 62 (24), pp.6649-6666. ⟨10.1021/acs.jcim.2c00337⟩

Article dans une revue hal-03624169v1

On the Quantum Chemical Nature of Lead(II) "Lone Pair

Christophe Gourlaouen , Jean-Philip Piquemal

Molecules, 2022, 27 (1), pp.27. ⟨10.3390/molecules27010027⟩

Article dans une revue hal-03232340v1

Development of the Quantum Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed Phase Molecular Dynamics Simulations.

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Journal of Chemical Theory and Computation, 2022, 18 (6), pp.3607-3621. ⟨10.1021/acs.jctc.2c00029⟩

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Accurate Deep Learning-aided Density-free Strategy for Many-Body Dispersion-corrected Density Functional Theory

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Journal of Physical Chemistry Letters, 2022, 13 (19), pp.4381-4388. ⟨10.1021/acs.jpclett.2c00936⟩

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Improving Condensed Phase Water Dynamics with Explicit Nuclear Quantum Effects: the Polarizable Q-AMOEBA Force Field

Nastasia Mauger , Thomas Plé , Louis Lagardère , Simon Huppert , Jean-Philip Piquemal

Journal of Physical Chemistry B, 2022, ⟨10.1021/acs.jpcb.2c04454⟩

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Computationally driven discovery of SARS-CoV-2 M pro inhibitors: from design to experimental validation

Léa El Khoury , Zhifeng Jing , Daniele Loco , Alberto Cuzzolin , Alessandro Deplano et al.

Chemical Science, 2022, 13 (13), ⟨10.1039/d1sc05892d⟩

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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 , P. Monmarché et al.

Journal of Chemical Theory and Computation, 2022, 18 (2), pp.968-977. ⟨10.1021/acs.jctc.1c01024⟩

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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

ChemPhysChem, 2022, 23, pp.e202200349. ⟨10.1002/cphc.202200349⟩

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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 of Chemical Theory and Computation, 2022, 8 (3), pp.1633-1645. ⟨10.1021/acs.jctc.1c01291⟩

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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 , Chengwen Liu et al.

Journal of Physical Chemistry Letters, 2021, 12, pp.6218-6226. ⟨10.1021/acs.jpclett.1c01460⟩

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Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

Rae Corrigan , Guowei Qi , Andrew Thiel , Jack Lynn , Brandon D Walker et al.

Journal of Chemical Theory and Computation, 2021, ⟨10.1021/acs.jctc.0c01286⟩

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NCIPLOT and the analysis of noncovalent interactions using the reduced density gradient

Rubén Laplaza , Francesca Peccati , Roberto A. Boto , Chaoyu Quan , Alessandra Carbone et al.

Wiley Interdisciplinary Reviews: Computational Molecular Science, 2021, 11 (2), pp.e1497. ⟨10.1002/wcms.1497⟩

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

Journal of Chemical Theory and Computation, 2021, 17 (5), pp.3235-3236. ⟨10.1021/acs.jctc.1c00405⟩

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NCIPLOT and the analysis of noncovalent interactions using the reduced density gradient

Rubén Laplaza , Francesca Peccati , Roberto A. Boto , Chaoyu Quan , Alessandra Carbone et al.

Wiley Interdisciplinary Reviews: Computational Molecular Science, 2021, 11 (2), ⟨10.1002/wcms.1497⟩

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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 , G. Andrés Cisneros

The Journal of Chemical Physics, 2021, ⟨10.1063/5.0072380⟩

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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 of Chemical Theory and Computation, 2021, 17 (5), pp.2759-2774. ⟨10.1021/acs.jctc.0c01337⟩

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High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling

Théo Jaffrelot Inizan , Frederic Célerse , Olivier Adjoua , Dina El Ahdab , Luc-Henri Jolly et al.

Chemical Science, 2021, 12 (13), pp.4889-4907. ⟨10.1039/D1SC00145K⟩

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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 , Luc-Henri Jolly , Arnaud Durocher , Thibaut Véry et al.

Journal of Chemical Theory and Computation, 2021, 17 (4), pp.2034-2053. ⟨10.1021/acs.jctc.0c01164⟩

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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 of Physical Chemistry Letters, 2021, 12 (34), pp.8285-829. ⟨10.1021/acs.jpclett.1c01722⟩

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Atomistic Polarizable embeddings: energy, dynamics, spectroscopy and reactivity.

Daniele Loco , Louis Lagardère , Olivier Adjoua , Jean-Philip Piquemal

Accounts of Chemical Research, 2021, ⟨10.1021/acs.accounts.0c00662⟩

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Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential

Chengwen Liu , Jean-Philip Piquemal , Pengyu Ren

Journal of Physical Chemistry Letters, 2020, 11 (2), pp.419-426. ⟨10.1021/acs.jpclett.9b03489⟩

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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 , Laurent Salmon , N. Gresh

Journal of Computational Chemistry, 2020, 41 (8), pp.839-854. ⟨10.1002/jcc.26134⟩

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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 of Chemical Theory and Computation, 2020, 16 (4), pp.2013 - 2020. ⟨10.1021/acs.jctc.9b01204⟩

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A New Way for Probing Bond Strength

J. Klein , H. Khartabil , Jean-Charles Boisson , J. Contreras-Garcia , Jean-Philip Piquemal et al.

Journal of Physical Chemistry A, 2020, 124 (9), pp.1850-1860. ⟨10.1021/acs.jpca.9b09845⟩

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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

Chemical Communications, 2020, 56, pp.6632-6635. ⟨10.1039/D0CC01938K⟩

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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.

Frontiers in Chemistry, 2020, 8, pp.440. ⟨10.3389/fchem.2020.00440⟩

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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 , Jean-Philip Piquemal

The Journal of Chemical Physics, 2020, 153, pp.024101. ⟨10.1063/5.0005060⟩

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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 of Chemical Theory and Computation, 2020, ⟨10.1021/acs.jctc.0c00063⟩

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

Marion Devillers , Jean‐philip Piquemal , Laurent Salmon , Nohad Gresh

Journal of Computational Chemistry, 2020, 41 (8), pp.839-854. ⟨10.1002/jcc.26134⟩

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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 et al.

PeerJ Physical Chemistry, 2019, 1, pp.e6. ⟨10.7717/peerj-pchem.6⟩

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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 of Chemical Theory and Computation, 2019, 15 (6), pp.3694-3709. ⟨10.1021/acs.jctc.9b00199⟩

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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 , Giovanni Scalmani , Paolo Gatto , Eric Cancès et al.

International Journal of Quantum Chemistry, 2019, 119, pp.e25669. ⟨10.1002/qua.25669⟩

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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 of Physical Chemistry Letters, 2019, 10 (10), pp.2593−2599. ⟨10.1021/acs.jpclett.9b00901⟩

Article dans une revue 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 et al.

Annual Reviews of Biophysics, 2019, 48, pp.371-394. ⟨10.1146/annurev-biophys-070317-033349⟩

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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 of Chemical Theory and Computation, 2019, ⟨10.1021/acs.jctc.9b00721⟩

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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.

Chemical Science, 2019, ⟨10.1039/C9SC01745C⟩

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

Dmitry Bedrov , Jean-Philip Piquemal , Oleg V. Borodin , Alexander Mackerell , Benoît Roux et al.

Chemical Reviews, 2019, ⟨10.1021/acs.chemrev.8b00763⟩

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Accurate biomolecular simulations account for electronic polarization

Josef Melcr , Jean-Philip Piquemal

Frontiers in Molecular Biosciences, 2019, 6, pp.143. ⟨10.3389/fmolb.2019.00143⟩

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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.

Living Journal of Computational Molecular Science, 2019, 1 (2), ⟨10.33011/livecoms.1.2.10409⟩

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AMOEBA+ Classical Potential for Modeling Molecular Interactions

Chengwen Liu , Jean-Philip Piquemal , Pengyu Ren

Journal of Chemical Theory and Computation, 2019, ⟨10.1021/acs.jctc.9b00261⟩

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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.

ChemPhysChem, 2018, 19 (6), pp.724-735. ⟨10.1002/cphc.201701325⟩

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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 of Physical Chemistry B, 2018, 122 (24), pp.6371-6376. ⟨10.1021/acs.jpcb.8b03194⟩

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

Benjamin Stamm , Louis Lagardere , Etienne Polack , Yvon Maday , Jean-Philip Piquemal

The Journal of Chemical Physics, 2018, 149 (12), pp.124103. ⟨10.1063/1.5044541⟩

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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 of Chemical Theory and Computation, 2018, 14 (4), pp.2084-2108. ⟨10.1021/acs.jctc.7b01169⟩

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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

Journal of Physical Chemistry Letters, 2018, 9 (11), pp.3062-3067. ⟨10.1021/acs.jpclett.8b01412⟩

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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 , Aurélien de la Lande

Journal of Chemical Theory and Computation, 2018, 14 (5), pp.2705-2720. ⟨10.1021/acs.jctc.7b01128⟩

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Tinker 8: Software Tools for Molecular Design

Joshua A Rackers , Zhi Wang , Chao Lu , Marie L Laury , Louis Lagardere et al.

Journal of Chemical Theory and Computation, 2018, 14 (10), pp.5273-5289. ⟨10.1021/acs.jctc.8b00529⟩

Article dans une revue 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 , Benjamin Stamm et al.

Chemical Science, 2018, 9, pp.956-972 ⟨10.1039/C7SC04531J⟩

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Capturing Many-Body Interactions with Classical Dipole Induction Models

Chengwen Liu , Rui R. Qi , Qiantao Qi , J.-P. Piquemal , Pengyu Ren

Journal of Chemical Theory and Computation, 2017, 13 (6), pp.2751-2761. ⟨10.1021/acs.jctc.7b00225⟩

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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.

Biochemical and Biophysical Research Communications, 2017, ⟨10.1016/j.bbrc.2017.05.001⟩

Article dans une revue hal-01520237v1
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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

Article dans une revue hal-01521838v1
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Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs

Matthew Harger , Daniel Li , Zhi Wang , Kevin Dalby , Louis Lagardère et al.

Journal of Computational Chemistry, 2017, 38 (23), pp.2047-2055. ⟨10.1002/jcc.24853⟩

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An Optimized Charge Penetration Model for Use with the AMOEBA Force Field

Joshua A. Rackers , Qiantao Wang , Chengwen Liu , Jean-Philip Piquemal , Pengyu Ren et al.

Physical Chemistry Chemical Physics, 2017, ⟨10.1039/C6CP06017J⟩

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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 of Computational Chemistry, 2017, 121, pp.3997 - 1920. ⟨10.1021/acs.jpcb.7b01836⟩

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Channeling Through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li <sup>+</sup> , Na <sup>+</sup> , K <sup>+</sup> 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 of Physical Chemistry B, 2017, ⟨10.1021/acs.jpcb.7b01836⟩

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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

The Journal of Chemical Physics, 2017, 147 (16), pp.161724. ⟨10.1063/1.4985911⟩

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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 , Mirna Damergi , Serge Nader , Léa El Khoury , Zeina Hobaika et al.

Journal of Physical Chemistry B, 2017, 121 (26), pp.6295-6312. ⟨10.1021/acs.jpcb.7b01053⟩

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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

Article dans une revue hal-01636270v1
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Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding

Daniele Loco , Louis Lagardère , Stefano Caprasecca , Filippo Lipparini , Benedetta Mennucci et al.

Journal of Chemical Theory and Computation, 2017, ⟨10.1021/acs.jctc.7b00572⟩

Article dans une revue hal-01571619v2

Preface: Special Topic: From Quantum Mechanics to Force Fields

Jean-Philip Piquemal , Kenneth Jordan

The Journal of Chemical Physics, 2017, 147 (16), pp.161401. ⟨10.1063/1.5008887⟩

Article dans une revue hal-02127251v1
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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.

ACS Omega, 2017, 2 (7), pp.3467-3474. ⟨10.1021/acsomega.7b00471⟩

Article dans une revue hal-02126840v1
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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 , Benjamin Stamm , Yvon Maday , Pengyu Ren et al.

Journal of Chemical Theory and Computation, 2017, 13 (1), pp.180-190. ⟨10.1021/acs.jctc.6b00981⟩

Article dans une revue hal-01395833v4
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Butanethiol adsorption and dissociation on Ag (111): A periodic DFT study

Aixiao Li , Jean-Philip Piquemal , Johannes Richardi , Monica Calatayud

Surface Science : A Journal Devoted to the Physics and Chemistry of Interfaces, 2016, 646, pp.247-252. ⟨10.1016/j.susc.2015.06.009⟩

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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

Journal of Computational Chemistry, 2016, ⟨10.1002/jcc.24295⟩

Article dans une revue 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 of Chemical Theory and Computation, 2016, 12 (8), pp.3654-3661. ⟨10.1021/acs.jctc.6b00385⟩

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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 of Computational Chemistry, 2016, 37 (32), pp.2770-2782. ⟨10.1002/jcc.24503⟩

Article dans une revue istex hal-02126855v1
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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 of Computational Chemistry, 2016, 37 (5), pp.494-506. ⟨10.1002/jcc.24257⟩

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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

Chemical Physics Letters, 2015, 637, pp.51-57. ⟨10.1016/j.cplett.2015.07.047⟩

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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 of Computational Chemistry, 2015, 36 (5), pp.285-302. ⟨10.1002/jcc.23801⟩

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Could the “Janus-like” properties of the halobenzene CX bond (XCl, Br) be leveraged to enhance molecular recognition?

Krystel El Hage , Jean-Philip Piquemal , Zeina Hobaika , Richard G. Maroun , Nohad Gresh

Journal of Computational Chemistry, 2015, 36 (4), pp.210-221. ⟨10.1002/jcc.23786⟩

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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 of Chemical Theory and Computation, 2015, 11 (2), pp.623-634. ⟨10.1021/ct500998q⟩

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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 , J. E. Sponer , M. Devereux , B. De Courcy , Jean-Philip Piquemal et al.

Journal of Physical Chemistry B, 2015, 119 (30), pp. 9477-9495. ⟨10.1021/acs.jpcb.5b01695⟩

Article dans une revue hal-01287484v1
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Interpretation of the reduced density gradient

Roberto A. Boto , Julia Contreras-García , Julien Tierny , Jean-Philip Piquemal

Molecular Physics, 2015, pp.1-9. ⟨10.1080/00268976.2015.1123777⟩

Article dans une revue hal-01253888v1
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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 of Chemical Theory and Computation, 2015, 11 (6), pp.2609-2618. ⟨10.1021/acs.jctc.5b00267⟩

Article dans une revue hal-01287207v1
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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 et al.

Journal of the American Chemical Society, 2015, 137 (3), pp.1141-1146. ⟨10.1021/ja510259p⟩

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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 of Computational Chemistry, 2015, 36 (15), pp.1167-1175. ⟨10.1002/jcc.23911⟩

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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 of Chemical Theory and Computation, 2015, 11 (6), pp.2589-2599. ⟨10.1021/acs.jctc.5b00171⟩

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Characterizing Molecular Interactions in Chemical Systems

David Guenther , Roberto Alvarez-Boto , Julia Contreras-Garcia , Jean-Philip Piquemal , Julien Tierny

IEEE Transactions on Visualization and Computer Graphics, 2014, 20 (12), pp.2476-2485. ⟨10.1109/TVCG.2014.2346403⟩

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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 et al.

Journal of Chemical Theory and Computation, 2014, 10 (4), pp.1638-1651. ⟨10.1021/ct401096t⟩

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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 of Computational Chemistry, 2014, 35 (29), pp.2096-2106. ⟨10.1002/jcc.23724⟩

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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 of Computational Chemistry, 2014, 35 (21), pp.1577-1591. ⟨10.1002/jcc.23661⟩

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DFT-steric-based energy decomposition analysis of intermolecular interactions

Dong Fang , Jean-Philip Piquemal , Shubin Liu , G. Andrés Cisneros

Theoretical Chemistry Accounts: Theory, Computation, and Modeling, 2014, 133 (5), ⟨10.1007/s00214-014-1484-7⟩

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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 of Chemical Theory and Computation, 2014, 10 (5), pp.1900-1909. ⟨10.1021/ct4006135⟩

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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 of Physical Chemistry Letters, 2014, 5, pp.953-958. ⟨10.1021/jz5002506⟩

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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.

The Journal of Chemical Physics, 2014, 141 (18), pp.184108. ⟨10.1063/1.4901304⟩

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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.

Physical Chemistry Chemical Physics, 2014, 16, pp.9876-9891. ⟨10.1039/C3CP52774C⟩

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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 of Molecular Modeling, 2014, 20 (11), ⟨10.1007/s00894-014-2472-5⟩

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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

Journal of Physical Chemistry A, 2014, 118 (41), pp.9772-9782. ⟨10.1021/jp5079899⟩

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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 of Physical Chemistry B, 2014, 118 (24), pp.6456-6465. ⟨10.1021/jp411671a⟩

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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 of Physical Chemistry A, 2014, 118 (35), pp.7598-7612. ⟨10.1021/jp5051657⟩

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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 of Chemical Theory and Computation, 2014, 10, pp.1361-1365. ⟨10.1021/ct500050p⟩

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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 of Molecular Modeling, 2014, 20, pp.2471. ⟨10.1007/s00894-014-2471-6⟩

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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.

Bioorganic and Medicinal Chemistry Letters, 2014, 24 (17), pp.4254-4259. ⟨10.1016/j.bmcl.2014.07.028⟩

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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

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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

Chemical Physics Letters, 2013, 563, pp.25-29. ⟨10.1016/j.cplett.2013.01.066⟩

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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 of Chemical Theory and Computation, 2013, 9 (5), pp.2416-2424. ⟨10.1021/ct300524v⟩

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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 of Chemical Theory and Computation, 2013, 9 (5), pp.2156-2160. ⟨10.1021/ct400130b⟩

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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

Canadian Journal of Chemistry, 2013, 91 (9), pp.821-831. ⟨10.1139/cjc-2012-0546⟩

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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

Canadian Journal of Chemistry, 2013, 91 (9), pp.804-810. ⟨10.1139/cjc-2012-0547⟩

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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

Journal of Chemical Theory and Computation, 2013, 9 (8), pp.3263-3266. ⟨10.1021/ct400420r⟩

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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

Journal of Computational Chemistry, 2013, 34 (13), pp.1125-1135. ⟨10.1002/jcc.23242⟩

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Ionic interactions: Comparative topological approach

Julia Contreras-García , Monica Calatayud , Jean-Philip Piquemal , J.M. Recio

Computational and Theoretical Chemistry, 2012, 998, pp.193-201. ⟨10.1016/j.comptc.2012.07.043⟩

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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 of Chemical Theory and Computation, 2012, 8 (4), pp.1314-1324. ⟨10.1021/ct200812y⟩

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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.

Theoretical Chemistry Accounts: Theory, Computation, and Modeling, 2012, 131 (March), pp.1198. ⟨10.1007/s00214-012-1198-7⟩

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From quantum mechanics to force fields: new methodologies for the classical simulation of complex systems

Jean-Philip Piquemal , Kenneth Jordan

Theoretical Chemistry Accounts: Theory, Computation, and Modeling, 2012, 131 (4), ⟨10.1007/s00214-012-1207-x⟩

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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 of Chemical Theory and Computation, 2012, 8 (11), pp.3993-3997. ⟨10.1021/ct300234g⟩

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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

Chemical Physics Letters, 2012, 532, pp.9-12. ⟨10.1016/j.cplett.2012.02.037⟩

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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 of Chemical Theory and Computation, 2011, 7 (3), pp.625-632. ⟨10.1021/ct100641a⟩

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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

Physical Chemistry Chemical Physics, 2011, 13 (23), pp.11239. ⟨10.1039/c0cp02550j⟩

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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 of Chemical Theory and Computation, 2011, 7 (3), pp.618-624. ⟨10.1021/ct1005938⟩

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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.

Catalysis Today, 2011, 177 (1), pp.79-86. ⟨10.1016/j.cattod.2011.07.015⟩

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Unraveling Low-Barrier Hydrogen Bonds in Complex Systems with a Simple Quantum Topological Criterion

Robin Chaudret , G. Andrés Cisneros , Olivier Parisel , Jean-Philip Piquemal

Chemistry - A European Journal, 2011, 17 (10), pp.2833-2837. ⟨10.1002/chem.201002978⟩

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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 of Computational Chemistry, 2011, 32 (14), pp.2949-2957. ⟨10.1002/jcc.21865⟩

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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.

Proteins - Structure, Function and Bioinformatics, 2011, 79 (1), pp.203-220. ⟨10.1002/prot.22873⟩

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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 of Computational Chemistry, 2011, 32 (6), pp.1178-1182. ⟨10.1002/jcc.21698⟩

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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 of Physical Chemistry B, 2011, 115 (25), pp.8304-8316. ⟨10.1021/jp2024654⟩

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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

International Journal of Quantum Chemistry, 2011, 111 (6), pp.1213-1221. ⟨10.1002/qua.22760⟩

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Enforcing hemidirectionality in Pb(II) complexes: The importance of anionic ligands

M.-C. van Severen , J.-P. Piquemal , O. Parisel

Chemical Physics Letters, 2011, 510 (1-3), pp.27-30. ⟨10.1016/j.cplett.2011.04.096⟩

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Editorial: Special issue on quantum mechanical modeling of biological systems

Jean-Philip Piquemal , Dennis R. Salahub

INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 2010, 2 (1), pp.1-2. ⟨10.1007/s12539-010-0001-5⟩

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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 of Physical Chemistry B, 2010, 114 (14), pp.4884-4895. ⟨10.1021/jp907629k⟩

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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

Journal of Chemical Theory and Computation, 2010, 6 (7), pp.2059-2070. ⟨10.1021/ct100091j⟩

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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

INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 2010, 2 (1), pp.3-11. ⟨10.1007/s12539-010-0096-8⟩

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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 of Chemical Theory and Computation, 2010, 6 (4), pp.1048-1063. ⟨10.1021/ct100089s⟩

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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

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Importance of backdonation in [M–(CO)]p+ complexes isoelectronic to [Au–(CO)]+

C. Gourlaouen , O. Parisel , J.-P. Piquemal

The Journal of Chemical Physics, 2010, 133 (12), pp.124310. ⟨10.1063/1.3491266⟩

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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

Journal of Chemical Theory and Computation, 2010, 7 (1), pp.138-147. ⟨10.1021/ct1004005⟩

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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 of the American Chemical Society, 2010, 132 (34), pp.11860-3. ⟨10.1021/ja103996q⟩

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Lead Substitution in Synaptotagmin: A Case Study

M.-C. van Severen , J.-P. Piquemal , O. Parisel

Journal of Physical Chemistry B, 2010, 114 (11), pp.4005-4009. ⟨10.1021/jp910131r⟩

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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

Bioorganic and Medicinal Chemistry, 2009, 17 (20), pp.7100-7107. ⟨10.1016/j.bmc.2009.09.005⟩

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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.

Inorganic Chemistry, 2009, 48 (15), pp.7003-7005. ⟨10.1021/ic900567z⟩

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Gaussian Multipole Model (GMM)

Dennis Elking , G. Andrés Cisneros , Jean-Philip Piquemal , Thomas Darden , Lee Pedersen

Journal of Chemical Theory and Computation, 2009, 6 (1), pp.190-202. ⟨10.1021/ct900348b⟩

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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

INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 2009, 1 (1), pp.55-60. ⟨10.1007/s12539-008-0027-0⟩

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Trends in ns2np0 [M(CO)]q+ complexes: From germanium to element 114 (Uuq)

C. Gourlaouen , O. Parisel , J.-P. Piquemal

Chemical Physics Letters, 2009, 469 (1-3), pp.38-42. ⟨10.1016/j.cplett.2008.12.040⟩

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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.

AIP Conference Proceedings, 2009, 1102, pp.185-192. ⟨10.1063/1.3108373⟩

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Beyond holo/hemidirectionality in Pb(II) complexes: Can the valence lone pair be bisdirected?

M. van Severen , J.-P. Piquemal , O. Parisel

Chemical Physics Letters, 2009, 478 (1-3), pp.17-19. ⟨10.1016/j.cplett.2009.07.036⟩

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New intermolecular benchmark calculations on the water dimer: SAPT and supermolecular post-Hartree-Fock approaches

P. Reinhardt , J-P. Piquemal

International Journal of Quantum Chemistry, 2009, 109 (14), pp.3259-3267. ⟨10.1002/qua.22299⟩

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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.

International Journal of Quantum Chemistry, 2008, 108 (11), pp.1951-1969. ⟨10.1002/qua.21711⟩

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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

Chemistry - A European Journal, 2008, 14 (9), pp.2730-2743. ⟨10.1002/chem.200701265⟩

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Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments

Julien Pilmé , Jean-Philip Piquemal

Journal of Computational Chemistry, 2008, 29 (9), pp.1440-1449. ⟨10.1002/jcc.20904⟩

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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.

International Journal of Quantum Chemistry, 2008, 108 (11), pp.1905-1912. ⟨10.1002/qua.21675⟩

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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 of Chemical Theory and Computation, 2008, 4 (10), pp.1659-1668. ⟨10.1021/ct800200j⟩

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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 of Chemical Theory and Computation, 2008, 4 (12), pp.2020-2029. ⟨10.1021/ct800242n⟩

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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

Journal of Computational Chemistry, 2007, 28 (5), pp.938-957. ⟨10.1002/jcc.20586⟩

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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

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Toward a Separate Reproduction of the Contributions to the Hartree−Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential

Jean-Philip Piquemal , Hilaire Chevreau , Nohad Gresh

Journal of Chemical Theory and Computation, 2007, 3 (3), pp.824-837. ⟨10.1021/ct7000182⟩

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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

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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

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Numerical Fitting of Molecular Properties to Hermite Gaussians

G. Andrés Cisneros , Dennis Elking , Jean-Philip Piquemal , Thomas Darden

Journal of Physical Chemistry A, 2007, 111 (47), pp.12049-12056. ⟨10.1021/jp074817r⟩

Article dans une revue hal-02126812v1

Key Role of the Polarization Anisotropy of Water in Modeling Classical Polarizable Force Fields

Jean-Philip Piquemal , Riccardo Chelli , Piero Procacci , Nohad Gresh

Journal of Physical Chemistry A, 2007, 111 (33), pp.8170-8176. ⟨10.1021/jp072687g⟩

Article dans une revue istex hal-02126880v1

Towards a force field based on density fitting

Nohad Gresh , J.-P. Piquemal , G. Andres Cisneros , P. Reinhardt , T.A. Darden

The Journal of Chemical Physics, 2006, 124, pp.104101

Article dans une revue hal-00494627v1

[Pb(H2O)]2+ and [Pb(OH)]+: Four-component density functional theory calculations, correlated scalar relativistic constrained-space orbital variation energy decompositions, and topological analysis

Christophe Gourlaouen , Jean-Philip Piquemal , Olivier Parisel

The Journal of Chemical Physics, 2006, 124 (17), pp.174311. ⟨10.1063/1.2186994⟩

Article dans une revue hal-02127222v1

Quantum Mechanics/Molecular Mechanics Electrostatic Embedding with Continuous and Discrete Functions

G. Andrés Cisneros , Jean-Philip Piquemal , Thomas Darden

Journal of Physical Chemistry B, 2006, 110 (28), pp.13682-13684. ⟨10.1021/jp062768x⟩

Article dans une revue hal-02126805v1

Comments on the nature of the bonding in oxygenated dinuclear copper enzyme models

Jean-Philip Piquemal , Julien Pilmé

Journal of Molecular Structure: THEOCHEM, 2006, 764 (1-3), pp.77 - 86. ⟨10.1016/j.theochem.2006.02.013⟩

Article dans une revue hal-01906896v1

Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

Jean-Philip Piquemal , Lalith Perera , G. Andrés Cisneros , Pengyu Ren , Lee Pedersen et al.

The Journal of Chemical Physics, 2006, 125 (5), pp.054511. ⟨10.1063/1.2234774⟩

Article dans une revue hal-02126806v1

Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods

G. Andrés Cisneros , Jean-Philip Piquemal , Thomas Darden

The Journal of Chemical Physics, 2006, 125 (18), pp.184101. ⟨10.1063/1.2363374⟩

Article dans une revue hal-02126808v1

Revisiting the geometry of nd10 (n+1)s0 [M(H2O)]p+ complexes using four-component relativistic DFT calculations and scalar relativistic correlated CSOV energy decompositions (Mp+ = Cu+, Zn2+, Ag+, Cd2+, Au+, Hg2+)

Christophe Gourlaouen , Jean-Philip Piquemal , Trond Saue , Olivier Parisel

Journal of Computational Chemistry, 2006, 27 (2), pp.142-156. ⟨10.1002/jcc.20329⟩

Article dans une revue istex hal-02127159v1

Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-β-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry

Jens Antony , Jean-Philip Piquemal , Nohad Gresh

Journal of Computational Chemistry, 2005, 26 (11), pp.1131-1147. ⟨10.1002/jcc.20245⟩

Article dans une revue hal-02127145v1

Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations

Nohad Gresh , Jean-Philip Piquemal , Morris Krauss

Journal of Computational Chemistry, 2005, 26 (11), pp.1113-1130. ⟨10.1002/jcc.20244⟩

Article dans une revue hal-02127150v1

A CSOV study of the difference between HF and DFT intermolecular interaction energy values: The importance of the charge transfer contribution

Jean-Philip Piquemal , Antonio Marquez , Olivier Parisel , Claude Giessner-Prettre

Journal of Computational Chemistry, 2005, 26 (10), pp.1052-1062. ⟨10.1002/jcc.20242⟩

Article dans une revue hal-02126803v1

Intermolecular electrostatic energies using density fitting

G. Andrés Cisneros , Jean-Philip Piquemal , Thomas Darden

The Journal of Chemical Physics, 2005, 123 (4), pp.044109. ⟨10.1063/1.1947192⟩

Article dans une revue hal-02126804v1

Theoretical study of phenol and 2-aminophenol docking at a model of the tyrosinase active site

Jean-Philip Piquemal , Jacques Maddaluno , Bernard Silvi , Claude Giessner-Prettre

New Journal of Chemistry, 2003, 27 (6), pp.909-913. ⟨10.1039/B210307A⟩

Article dans une revue hal-02126801v1

Improved Formulas for the Calculation of the Electrostatic Contribution to the Intermolecular Interaction Energy from Multipolar Expansion of the Electronic Distribution

Jean-Philip Piquemal , Nohad Gresh , Claude Giessner-Prettre

Journal of Physical Chemistry A, 2003, 107 (48), pp.10353-10359. ⟨10.1021/jp035748t⟩

Article dans une revue hal-02126882v1

Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF

Jean-Philip Piquemal , Ben Williams-Hubbard , Natalie Fey , Robert Deeth , Nohad Gresh et al.

Journal of Computational Chemistry, 2003, 24 (16), pp.1963-1970. ⟨10.1002/jcc.10354⟩

Article dans une revue hal-02127138v1

VTX: High-performance molecular structure and dynamics visualization software

Maxime Maria , Simon Guionnière , Nicolas Dacquay , Yassine Naïmi , Jean-Philip Piquemal et al.

8th chemoinformatics Strasbourg summer school, Jun 2022, Strasbourg, France

Communication dans un congrès hal-03778760v1

Unraveling interactions in large complex systems using quantum chemistry interpretative techniques and new generation polarizable force fields

R. Chaudret , B. de Courcy , A. Marjolin , M.-C. van Severen , P. Ren et al.

INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2009: (ICCMSE 2009), 2009, Rhodes, Greece. pp.699-702

Communication dans un congrès hal-02126865v1
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FeNNix-Bio1 : un modèle de fondation pour les simulations atomistiques précises en Drug Design

Olivier Adjoua , Louis Lagardère , Jean-Philip Piquemal , Thomas Plé , Anouar Benali et al.

Grand Challenges Jean Zay 4, GENCI, pp.22-25, 2025

Chapitre d'ouvrage hal-05428979v1
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Polarizable Multiscale Dynamics for probing solvent and complex environments

Daniele Loco , Jean-Philip Piquemal

Stefano Crespi; Stefano Protti. Photochemistry, 50, Royal Society of Chemistry, pp.382-398, 2022, 978-1-83916-768-3. ⟨10.1039/9781839167676-00386⟩

Chapitre d'ouvrage hal-03698342v1
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A complete NCI perspective: from new bonds to reactivity

Christophe Narth , Zeina Maroun , Roberto A. Boto , Robin Chaudret , Marie-Laure Bonnet et al.

Esmail Alikhani, Remi Chauvin, Christine Lepetit, Bernard Silvi. Applications of Topological Methods in Molecular Chemistry, 22, Springer, pp.491-527, 2016, Challenges and Advances in Computational Chemistry and Physics ⟨10.1007/978-3-319-29022-5_18⟩

Chapitre d'ouvrage hal-01224203v1
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Status of the Gaussian Electrostatic Model, a Density-Based Polarizable Force Field

Jean-Philip Piquemal , G. Andrés Cisneros

Qiang Cui, Pengyu Ren and Markus Meuwly. Many-body effects and electrostatics, 28, Pan Standford Publishing, pp.269-299, 2016, multi-scale computations of Biomolecules, 9789814613927. ⟨10.1201/b21343-11⟩

Chapitre d'ouvrage hal-01114075v1
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Addressing the issues of non-isotropy and non-additivity in the development of quantum chemistry-grounded polarizable molecular mechanics.

Nohad Gresh , Krystel El Hage , Elodie Goldwaser , Benoit De Courcy , Robin Chaudret et al.

J. L. Rivail, M. Ruiz-Lopez, X. Assfeld. Quantum Modeling of Complex Molecular Systems, 21, Springer, pp.1-49, 2015, ⟨10.1007/978-3-319-21626-3_1⟩

Chapitre d'ouvrage hal-01104542v1
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Polarizable Force Fields for Biomolecular Modeling

Yue Shi , Pengyu Ren , Michael Schnieders , Jean-Philip Piquemal

Reviews in Computational Chemistry, 28 (51), Wiley, 2015, ⟨10.1002/9781118889886.ch2⟩

Chapitre d'ouvrage hal-01114184v1

Design Of Next Generation Force Fields From AB Initio Computations: Beyond Point Charges Electrostatics

G.A. Cisneros , T.A. Darden , N. Gresh , J. Pilme , P. Reinhardt et al.

Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications, Springer Netherlands, pp.137-172, 2009

Chapitre d'ouvrage hal-02127328v1