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Force field Polarizable force field High performance computing HPC Intermolecular interactions Molecular dynamics MD Quantum chemistry Molecular modeling Energy decomposition analysis Polarizable force fields Dolutegravir HIV-1 ELF Force fields Applied mathematics Polarizable force field AMOEBA Molecular dynamics SIBFA Conjugate gradient algorithm QM/MM Topological analysis
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CV of Jean-Philip Piquemal

Jean-Philip Piquemal

Sorbonne Université (SU), Laboratoire de Chimie Théorique, UMR 7616 CNRS, 

Tour 12-13, 4ème étage, 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 

(last update: 09/2020)

 

Present position

- Distinguished Professor (EXceptional class, PREX1) of Theoretical Chemistry, Sorbonne Université (Paris, France) .

- Director of the Laboratoire de Chimie Théorique, UMR 7616 Sorbonne Université & CNRS, Department of Chemistry.

- Junior member of the Institut Universitaire de France (IUF) 2016-2021.

- Research Adjunct Professor, Department of Biomedical Engineering, The University of Texas at Austin (USA).

- Editor, Results in Chemistry (Elsevier)

  

See Updated list/full publication Metrics on Google scholar: https://scholar.google.fr/citations?user=z0cOrb0AAAAJ&hl=fr

or Researcher ID: http://www.researcherid.com/rid/B-9901-2009 or visit my webpage : http://piquemalresearch.com/publications/

Professional background 

  • 2019-present     : Distinguished Professor (Exceptional class, PREX-1), CNU section 31, SU.
  • 2019-present     : Director Laboratoire de Chimie Théorique (LCT), Department of Chemistry, SU & CNRS
  • 2019-present     : Team leader: Extreme-scale Mathematically-based Computational Chemistry (EMC2), LCT, SU/CNRS.
  • 2019-present     : PI of the EMC2 ERC Synergy project (2019-2025) 
  • 2016-present     : Junior Member of the Institut Universitaire de France (junior chair 2016-2021)
  • 2015-present     : Research Adjunct Professor, Department of Biomedical Engineering, The University of Texas at Austin (USA).
  • 2016-2019         : Full Professor, first class (CNU section 31), SU.
  • 2012-2019         : Team leader of the MC2 interdisciplinary project team at ISCD (Institute for Computations and data), SU.
  • 2012-2018         : Director of the Institut Parisien de Chimie Physique et Théorique (IP2CT), FR 2622, SU & CNRS.
  • 2012-2018         : Team leader: research axis of LCT: «From quantum interpretative techniques to multiscale modeling». 
  • 2011-2016         : Full Professor (second class), UPMC.
  • 2009-2011         : Maître de Conférences - HDR (Associate Professor), UPMC (Research Habilitation (HDR), september 2009).  
  • 2006-2009         : Maître de Conférences (Assistant Professor), UPMC.
  • 2004-2006         : NIH Visiting Fellow, NIEHS, Research Triangle Park, NC, USA (group of Thomas Darden).

Education

  • 2011                  : Research Habilitation (HDR) in Theoretical Chemistry, UPMC.
  • 2001-2004         : Ph.D. Thesis (allocataire-moniteur) in Theoretical Chemistry, UPMC. [Academic Genealogy]
  • 2000-2001         : Diplôme d’Etude Approfondie (DEA) in Computational and Theoretical Chemistry UPMC. 
  • 1999-2000         : Master degree(Maîtrise) in Chemistry (major: Physical Chemistry), UPEC.

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

Teaching

Theoretical Chemistry (Quantum chemistry and Molecular Simulation), Computer Sciences, Physical Chemistry

Honors & Awards

  • 2020: i-Lab Innovation Award (French Ministry of Higher Education, Research and Innovation/Bpifrance)
  • 2019: ERC Synergy, Principal Investigator, project Extreme-scale Mathematically-based Computational Chemistry (EMC2 with E. Cancès, L. Grigori and Y. Maday)
  • 2018: Atos Joseph Fourier Prize in Numerical Simulation (1st prize)
  • 2018: France-Berkeley Fund Award
  • 2016: nominated as a Junior Member of the Institut Universitaire de France (junior chair 2016-2021)
  • 2012: Emergence-UPMC fund Award
  • 2011: Wiley-International Journal of Quantum Chemistry Young Investigator Award
  • 2008: France-Canada Research Fund Award

 Editorial activities

 Industry

Scientic societies memberships

  • Société Chimique de France (SFC)
  • American Chemical Society (ACS)
  • Association for Computing Machinery (ACM)
  • Sigma Xi

 

Preprints, Working Papers, ...3 documents

  • Christophe Gourlaouen, Jean-Philip Piquemal. On the Quantum Chemical Nature of Lead(II) "Lone Pair". 2021. ⟨hal-03232340⟩
  • Nastasia Mauger, Thomas Plé, Louis Lagardère, Sara Bonella, Etienne Mangaud, et al.. Nuclear Quantum Effects in liquid water at near classical computational cost using the adaptive Quantum Thermal Bath. 2021. ⟨hal-03132347⟩
  • Corentin Lefebvre, Johanna Klein, Hassan Khartabil, Jean-Philip Piquemal, Eric Hénon. Introducing the Bond Asymmetry Factor: a New Concept for Probing Chemical Bonds under Perturbations. 2021. ⟨hal-03242056⟩

Journal articles150 documents

  • Rubén Laplaza, Francesca Peccati, Roberto A. Boto, Chaoyu Quan, Alessandra Carbone, et al.. NCIPLOT and the analysis of noncovalent interactions using the reduced density gradient. WIREs Computational Molecular Science, 2021, 11 (2), pp.e1497. ⟨10.1002/wcms.1497⟩. ⟨hal-02921299⟩
  • Théo Jaffrelot Inizan, Frederic Célerse, Olivier Adjoua, Dina El Ahdab, Luc-Henri Jolly, et al.. High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling. Chemical Science , The Royal Society of Chemistry, 2021, 12, pp.4889-4907. ⟨10.1039/D1SC00145K⟩. ⟨hal-02943694⟩
  • Frédéric Célerse, Louis Lagardère, Etienne Derat, Jean-Philip Piquemal. Correction to “Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Nonpolarizable Simulations of Realistic Systems”. Journal of Chemical Theory and Computation, American Chemical Society, 2021, 17 (5), pp.3235-3236. ⟨10.1021/acs.jctc.1c00405⟩. ⟨hal-03210774⟩
  • Olivier Adjoua, Louis Lagardère, Luc-Henri Jolly, Arnaud Durocher, Thibaut Véry, et al.. Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems. Journal of Chemical Theory and Computation, American Chemical Society, 2021, 17 (4), pp.2034-2053. ⟨10.1021/acs.jctc.0c01164⟩. ⟨hal-03179730⟩
  • Daniele Loco, Louis Lagardère, Olivier Adjoua, Jean-Philip Piquemal. Atomistic Polarizable embeddings: energy, dynamics, spectroscopy and reactivity.. Accounts of Chemical Research, American Chemical Society, 2021, ⟨10.1021/acs.accounts.0c00662⟩. ⟨hal-03210111⟩
  • Rae Corrigan, Guowei Qi, Andrew Thiel, Jack Lynn, Brandon Walker, et al.. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. Journal of Chemical Theory and Computation, American Chemical Society, 2021, ⟨10.1021/acs.jctc.0c01286⟩. ⟨hal-03183306⟩
  • Sehr Naseem-Khan, Nohad Gresh, Alston Misquitta, Jean-Philip Piquemal. Assessment of SAPT and Supermolecular EDAs Approaches for the Development of Separable and Polarizable force fields. Journal of Chemical Theory and Computation, American Chemical Society, 2021, 17 (5), pp.2759-2774. ⟨10.1021/acs.jctc.0c01337⟩. ⟨hal-02912013⟩
  • Dina El Ahdab, Louis Lagardère, Theo Jaffrelot Inizan, Frédéric Célerse, Chengwen Liu, et al.. Interfacial Water Many-body Effects Drive Structural Dynamics and Allosteric interactions in SARS-CoV-2 Main Protease Dimerization Interface. Journal of Physical Chemistry Letters, American Chemical Society, 2021, 12, pp.6218-6226. ⟨10.1021/acs.jpclett.1c01460⟩. ⟨hal-03220156⟩
  • Pierre Monmarché, Jeremy Weisman, Louis Lagardère, Jean-Philip Piquemal. Velocity jump processes : an alternative to multi-time-step methods for faster and accurate molecular dynamics simulations. Journal of Chemical Physics, American Institute of Physics, 2020, 153, pp.024101. ⟨10.1063/5.0005060⟩. ⟨hal-02314428⟩
  • Roberto Boto, Francesca Peccati, Rubén Laplaza, Chaoyu Quan, Alessandra Carbone, et al.. NCIPLOT4: fast, robust and quantitative analysis of noncovalent interactions. Journal of Chemical Theory and Computation, American Chemical Society, 2020, ⟨10.1021/acs.jctc.0c00063⟩. ⟨hal-02377999⟩
  • Daniele Loco, Riccardo Spezia, François Cartier, Isabelle Chataignier, Jean-Philip Piquemal. Solvation Effects Drive the Selectivity in Diels-Alder Reaction Under Hyperbaric Conditions. Chemical Communications, Royal Society of Chemistry, 2020, 56, pp.6632-6635. ⟨10.1039/D0CC01938K⟩. ⟨hal-02504716⟩
  • Léa El-Khoury, Frederic Célerse, Louis Lagardère, Luc-Henri Jolly, Etienne Derat, et al.. Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations. Journal of Chemical Theory and Computation, American Chemical Society, 2020, 16 (4), pp.2013 - 2020. ⟨10.1021/acs.jctc.9b01204⟩. ⟨hal-03046841⟩
  • Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren. Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential. Journal of Physical Chemistry Letters, American Chemical Society, 2020, 11 (2), pp.419-426. ⟨10.1021/acs.jpclett.9b03489⟩. ⟨hal-02410854⟩
  • J. Klein, H. Khartabil, J.C. Boisson, J. Contreras-Garcia, Jean-Philip Piquemal, et al.. A New Way for Probing Bond Strength. Journal of Physical Chemistry A, American Chemical Society, 2020, 124 (9), pp.1850-1860. ⟨10.1021/acs.jpca.9b09845⟩. ⟨hal-02377737⟩
  • M. Devillers, Jean-Philip Piquemal, L. Salmon, N. Gresh. Calibration of the dianionic phosphate group. Validation on the recognition site of the homodimeric enzyme phosphoglucose isomerase.. Journal of Computational Chemistry, Wiley, 2020, 41 (8), pp.839-854. ⟨10.1002/jcc.26134⟩. ⟨hal-02377726⟩
  • Perla El Darazi, Léa El Khoury, Krystel El Hage, Richard G. Maroun, Zeina Hobaika, et al.. Quantum-Chemistry based design of halobenzene derivatives with augmented affinities for the HIV-1 viral G4/C16 base-pair.. Frontiers in Chemistry, Frontiers Media, 2020, 8, pp.440. ⟨10.3389/fchem.2020.00440⟩. ⟨hal-02377718⟩
  • Luc-Henri Jolly, Alejandro Duran, Louis Lagardère, Jay W. Ponder, Pengyu Ren, et al.. Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0]. Living Journal of Computational Molecular Science, University of Colorado Boulder, 2019, 1 (2), ⟨10.33011/livecoms.1.2.10409⟩. ⟨hal-02147771v2⟩
  • Léa El-Khoury, Krystel El Hage, Jean-Philip Piquemal, Serge Fermandjian, Richard Maroun, et al.. Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities. PeerJ Physical Chemistry, PeerJ, 2019, 1, pp.e6. ⟨10.7717/peerj-pchem.6⟩. ⟨hal-02372493⟩
  • Louis Lagardère, Félix Aviat, Jean-Philip Piquemal. Pushing the limits of Multiple-Timestep Strategies for Polarizable Point Dipole Molecular Dynamics. Journal of Physical Chemistry Letters, American Chemical Society, 2019, 10 (10), pp.2593−2599. ⟨10.1021/acs.jpclett.9b00901⟩. ⟨hal-02119888⟩
  • Benjamin Stamm, Louis Lagardère, Giovanni Scalmani, Paolo Gatto, Eric Cancès, et al.. 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. International Journal of Quantum Chemistry, Wiley, 2019, 119, pp.e25669. ⟨10.1002/qua.25669⟩. ⟨hal-01793770⟩
  • Zhifeng Jing, Chengwen Liu, Sara Cheng, Rui Qi, Brandon Walker, et al.. Polarizable force fields for biomolecular simulations: Recent advances and applications. Annual Reviews of Biophysics, Annual Reviews, 2019, 48, pp.371-394. ⟨10.1146/annurev-biophys-070317-033349⟩. ⟨hal-01821899⟩
  • Dmitry Bedrov, Jean-Philip Piquemal, Oleg Borodin, Alexander Mackerell, Benoît Roux, et al.. Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields. Chemical Reviews, American Chemical Society, 2019, ⟨10.1021/acs.chemrev.8b00763⟩. ⟨hal-02144165⟩
  • Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren. AMOEBA+ Classical Potential for Modeling Molecular Interactions. Journal of Chemical Theory and Computation, American Chemical Society, 2019, ⟨10.1021/acs.jctc.9b00261⟩. ⟨hal-02142886⟩
  • Josef Melcr, Jean-Philip Piquemal. Accurate biomolecular simulations account for electronic polarization. Frontiers in Molecular Biosciences, Frontiers Media, 2019, 6, pp.143. ⟨10.3389/fmolb.2019.00143⟩. ⟨hal-02283625⟩
  • Poier Pier Paolo, Louis Lagardère, Jean-Philip Piquemal, Frank Jensen. Molecular Dynamics using Non-variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model. Journal of Chemical Theory and Computation, American Chemical Society, 2019, ⟨10.1021/acs.jctc.9b00721⟩. ⟨hal-02299827⟩
  • Daniele Loco, Louis Lagardère, G. Andrés Cisneros, Giovanni Scalmani, Michael Frisch, et al.. Towards Large Scale Hybrid QM/MM Dynamics of Complex Systems with Advanced Point Dipole Polarizable Embeddings. Chemical Science , The Royal Society of Chemistry, 2019, ⟨10.1039/C9SC01745C⟩. ⟨hal-02152908⟩
  • Frederic Célerse, Louis Lagardère, Etienne Derat, Jean-Philip Piquemal. Massively parallel implementation of Steered Molecular Dynamics in Tinker-HP: comparisons of polarizable and non-polarizable simulations of realistic systems. Journal of Chemical Theory and Computation, American Chemical Society, 2019, 15 (6), pp.3694-3709. ⟨10.1021/acs.jctc.9b00199⟩. ⟨hal-02122209⟩
  • Rui Qi, Zhifeng Jing, Chengwen Liu, Jean-Philip Piquemal, Kevin Dalby, et al.. Elucidating the Phosphate Binding Mode of Phosphate-Binding Protein: The Critical Effect of Buffer Solution. Journal of Physical Chemistry B, American Chemical Society, 2018, 122 (24), pp.6371-6376. ⟨10.1021/acs.jpcb.8b03194⟩. ⟨hal-02126853⟩
  • Benjamin Stamm, Louis Lagardere, Etienne Polack, Yvon Maday, Jean-Philip Piquemal. A coherent derivation of the Ewald summation for arbitrary orders of multipoles: The self-terms. Journal of Chemical Physics, American Institute of Physics, 2018, 149 (12), pp.124103. ⟨10.1063/1.5044541⟩. ⟨hal-01897263⟩
  • Louis Lagardère, Luc-Henri Jolly, Filippo Lipparini, Félix Aviat, Benjamin Stamm, et al.. Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields. Chemical Science , The Royal Society of Chemistry, 2018, 9, pp.956-972 ⟨10.1039/C7SC04531J⟩. ⟨hal-01648245v3⟩
  • Corentin Lefebvre, Hassan Khartabil, Jean-Charles Boisson, Julia Contreras-García, Jean-Philip Piquemal, et al.. The Independent Gradient Model: A New Approach for Probing Strong and Weak Interactions in Molecules from Wave Function Calculations. ChemPhysChem, Wiley-VCH Verlag, 2018, 19 (6), pp.724-735. ⟨10.1002/cphc.201701325⟩. ⟨hal-02126852⟩
  • Hatice Gökcan, Eric Kratz, Thomas Darden, Jean-Philip Piquemal, G. Andrés Cisneros. QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential. Journal of Physical Chemistry Letters, American Chemical Society, 2018, 9 (11), pp.3062-3067. ⟨10.1021/acs.jpclett.8b01412⟩. ⟨hal-02126841⟩
  • Changsheng Zhang, Chao Lu, Zhifeng Jing, Chuanjie Wu, Jean-Philip Piquemal, et al.. AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids. Journal of Chemical Theory and Computation, American Chemical Society, 2018, 14 (4), pp.2084-2108. ⟨10.1021/acs.jctc.7b01169⟩. ⟨hal-02126772⟩
  • Joshua Rackers, Zhi Wang, Chao Lu, Marie Laury, Louis Lagardere, et al.. Tinker 8: Software Tools for Molecular Design. Journal of Chemical Theory and Computation, American Chemical Society, 2018, 14 (10), pp.5273-5289. ⟨10.1021/acs.jctc.8b00529⟩. ⟨hal-01820747⟩
  • Xiaojing Wu, Carine Clavaguera, Louis Lagardère, Jean-Philip Piquemal, Aurelien de la Lande. AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms. Journal of Chemical Theory and Computation, American Chemical Society, 2018, 14 (5), pp.2705-2720. ⟨10.1021/acs.jctc.7b01128⟩. ⟨hal-02126731⟩
  • Matthew Harger, Daniel Li, Zhi Wang, Kevin Dalby, Louis Lagardère, et al.. Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs. Journal of Computational Chemistry, Wiley, 2017, 38 (23), pp.2047-2055. ⟨10.1002/jcc.24853⟩. ⟨hal-01571313⟩
  • Nohad Gresh, Sehr Naseem-Khan, Louis Lagardère, Jean-Philip Piquemal, Judit E. Sponer, et al.. 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. Journal of Physical Chemistry B, American Chemical Society, 2017, ⟨10.1021/acs.jpcb.7b01836⟩. ⟨hal-01502376⟩
  • Léa Khoury, Sehr Naseem-Khan, Karolina Kwapien, Zeina Hobaika, Richard Maroun, et al.. Importance of explicit smeared lone-pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange-repulsion and charge transfer contributions. Journal of Computational Chemistry, Wiley, 2017, 121, pp.3997 - 1920. ⟨10.1021/acs.jpcb.7b01836⟩. ⟨hal-01571959⟩
  • Félix Aviat, Antoine Levitt, Benjamin Stamm, Yvon Maday, Pengyu Ren, et al.. Truncated Conjugate Gradient (TCG): an optimal strategy for the analytical evaluation of the many-body polarization energy and forces in molecular simulations. Journal of Chemical Theory and Computation, American Chemical Society, 2017, 13 (1), pp.180-190. ⟨10.1021/acs.jctc.6b00981⟩. ⟨hal-01395833v4⟩
  • Daniele Loco, Louis Lagardère, Stefano Caprasecca, Filippo Lipparini, Benedetta Mennucci, et al.. Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding. Journal of Chemical Theory and Computation, American Chemical Society, 2017, ⟨10.1021/acs.jctc.7b00572⟩. ⟨hal-01571619v2⟩
  • Roberto Boto, Jean-Philip Piquemal, Julia Contreras-García. Revealing strong interactions with the reduced density gradient: a benchmark for covalent, ionic and charge-shift bonds. Theoretical Chemistry Accounts: Theory, Computation, and Modeling, Springer Verlag, 2017, 136, pp.139. ⟨hal-01636270⟩
  • Jean-Philip Piquemal, Kenneth Jordan. Preface: Special Topic: From Quantum Mechanics to Force Fields. Journal of Chemical Physics, American Institute of Physics, 2017, 147 (16), pp.161401. ⟨10.1063/1.5008887⟩. ⟨hal-02127251⟩
  • Léa El Khoury, Jean-Philip Piquemal, Serge Fermandjian, Richard G. Maroun, Nohad Gresh, et al.. The inhibition process of HIV-1 integrase by diketoacids molecules: Understanding the factors governing the better efficiency of dolutegravir. Biochemical and Biophysical Research Communications, Elsevier, 2017, ⟨10.1016/j.bbrc.2017.05.001⟩. ⟨hal-01520237⟩
  • Louis Lagardère, Léa El-Khoury, Sehr Naseem-Khan, Félix Aviat, Nohad Gresh, et al.. Towards scalable and accurate molecular dynamics using the SIBFA polarizable force field. AIP Conference Proceedings, American Institute of Physics, 2017. ⟨hal-01521838⟩
  • Chengwen Liu, Rui Qi, Qiantao Qi, J.-P. Piquemal, Pengyu Ren. Capturing Many-Body Interactions with Classical Dipole Induction Models. Journal of Chemical Theory and Computation, American Chemical Society, 2017, 13 (6), pp.2751-2761. ⟨10.1021/acs.jctc.7b00225⟩. ⟨hal-02126842⟩
  • Félix Aviat, Louis Lagardère, Jean-Philip Piquemal. The Truncated Conjugate Gradient (TCG), a Non-iterative/Fixed-cost Strategy for Computing Polarization in Molecular Dynamics: Fast Evaluation of Analytical Forces. Journal of Chemical Physics, American Institute of Physics, 2017, 147 (16), pp.161724. ⟨10.1063/1.4985911⟩. ⟨hal-01571663v2⟩
  • Krystel El Hage, Jean-Philip Piquemal, Nassima Oumata, Laurent Meijer, Hervé Galons, et al.. 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?. ACS Omega, ACS Publications, 2017, 2 (7), pp.3467-3474. ⟨10.1021/acsomega.7b00471⟩. ⟨hal-02126840⟩
  • Karolina Kwapien, Mirna Damergi, Serge Nader, Léa El Khoury, Zeina Hobaika, et al.. 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. Journal of Physical Chemistry B, American Chemical Society, 2017, 121 (26), pp.6295-6312. ⟨10.1021/acs.jpcb.7b01053⟩. ⟨hal-02126854⟩
  • Christophe Narth, Louis Lagardère, Etienne Polack, Nohad Gresh, Qiantao Wang, et al.. Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. Journal of Computational Chemistry, Wiley, 2016, 37 (5), pp.494-506. ⟨10.1002/jcc.24257⟩. ⟨hal-01223008⟩
  • Daniele Loco, Etienne Polack, Stefano Caprasecca, Louis Lagardère, Filippo Lipparini, et al.. A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations. Journal of Chemical Theory and Computation, American Chemical Society, 2016, 12 (8), pp.3654-3661. ⟨10.1021/acs.jctc.6b00385⟩. ⟨hal-02126716⟩
  • E. G. Kratz, L. Lagardere, F. Lipparini, J.-P. Piquemal, G. A. Cisneros. LICHEM: A QM/MM Program for Simulations with Multipolar and Polarizable Force Fields. Journal of Computational Chemistry, Wiley, 2016, ⟨10.1002/jcc.24295⟩. ⟨hal-01287204⟩
  • Nohad Gresh, David Perahia, Benoit de Courcy, Johanna Foret, Céline Roux, et al.. 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. Journal of Computational Chemistry, Wiley, 2016, 37 (32), pp.2770-2782. ⟨10.1002/jcc.24503⟩. ⟨hal-02126855⟩
  • Joshua A. Rackers, Qiantao Wang, Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren, et al.. An Optimized Charge Penetration Model for Use with the AMOEBA Force Field. Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2016, ⟨10.1039/C6CP06017J⟩. ⟨hal-01405847⟩
  • Aixiao Li, Jean-Philip Piquemal, Johannes Richardi, Monica Calatayud. Butanethiol adsorption and dissociation on Ag (111): A periodic DFT study. Surface Science, Elsevier, 2016, 646, pp.247-252. ⟨10.1016/j.susc.2015.06.009⟩. ⟨hal-01171804⟩
  • Filippo Lipparini, Louis Lagardère, Christophe Raynaud, Benjamin Stamm, Eric Cancès, et al.. Polarizable Molecular Dynamics in a Polarizable Continuum Solvent. Journal of Chemical Theory and Computation, American Chemical Society, 2015, 11 (2), pp.623-634. ⟨10.1021/ct500998q⟩. ⟨hal-01114784⟩
  • Qiantao Wang, Joshua A. Rackers, Chenfeng He, Rui Qi, Christophe Narth, et al.. A General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field. Journal of Chemical Theory and Computation, American Chemical Society, 2015, 11 (6), pp.2609-2618. ⟨10.1021/acs.jctc.5b00267⟩. ⟨hal-01287207⟩
  • Louis Lagardere, Filippo Lipparini, Etienne Polack, Benjamin Stamm, Eric Cancès, et al.. Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Towards Massively Parallel Computations using Smooth Particle Mesh Ewald. Journal of Chemical Theory and Computation, American Chemical Society, 2015, 11 (6), pp.2589-2599. ⟨10.1021/acs.jctc.5b00171⟩. ⟨hal-01223161⟩
  • N. Gresh, J. E. Sponer, M. Devereux, B. De Courcy, Jean-Philip Piquemal, et al.. Stacked and H-bonded cytosine dimers. Analysis of the intermolecular interaction energies by parallel quantum chemistry and polarizable molecular mechanics.. Journal of Physical Chemistry B, American Chemical Society, 2015, 119 (30), pp. 9477-9495. ⟨10.1021/acs.jpcb.5b01695⟩. ⟨hal-01287484⟩
  • Roberto A. Boto, Julia Contreras-García, Julien Tierny, Jean-Philip Piquemal. Interpretation of the reduced density gradient. Molecular Physics, Taylor & Francis, 2015, pp.1-9. ⟨10.1080/00268976.2015.1123777⟩. ⟨hal-01253888⟩
  • Benoit Courcy, Etienne Derat, Jean-Philip Piquemal. Bridging Organometallics and Quantum Chemical Topology: Understanding Electronic Relocalisation During Palladium-Catalyzed Reductive Elimination. Journal of Computational Chemistry, Wiley, 2015, 36 (15), pp.1167-1175. ⟨10.1002/jcc.23911⟩. ⟨hal-01397958⟩
  • Todor Dudev, Mike Devereux, Markus Meuwly, Carmay Lim, Jean-Philip Piquemal, et al.. Quantum-chemistry based calibration of the alkali metal cation series (Li + Cs + ) for large-scale polarizable molecular mechanics/dynamics simulations. Journal of Computational Chemistry, Wiley, 2015, 36 (5), pp.285-302. ⟨10.1002/jcc.23801⟩. ⟨hal-02126857⟩
  • Krystel El Hage, Jean-Philip Piquemal, Zeina Hobaika, Richard Maroun, Nohad Gresh. Approaching the double-faceted nature of the CX bond in halobenzenes with a bifunctional probe. Chemical Physics Letters, Elsevier, 2015, 637, pp.51-57. ⟨10.1016/j.cplett.2015.07.047⟩. ⟨hal-02126856⟩
  • Krystel El Hage, Jean-Philip Piquemal, Zeina Hobaika, Richard Maroun, Nohad Gresh. Could the “Janus-like” properties of the halobenzene CX bond (XCl, Br) be leveraged to enhance molecular recognition?. Journal of Computational Chemistry, Wiley, 2015, 36 (4), pp.210-221. ⟨10.1002/jcc.23786⟩. ⟨hal-02126858⟩
  • Ludivine Garcia, Federico Cisnetti, Natacha Gillet, Régis Guillot, Magali Aumont-Nicaise, et al.. Entasis Through Hook-and-Loop Fastening in a Glycoligand with Cumulative Weak Forces Stabilizing Cu(I).. Journal of the American Chemical Society, American Chemical Society, 2015, 137 (3), pp.1141-1146. ⟨10.1021/ja510259p⟩. ⟨hal-01101575⟩
  • Xiaojiao Mu, Qiantao Wang, Lee-Ping Wang, Stephen Fried, Jean-Philip Piquemal, et al.. Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field. Journal of Physical Chemistry B, American Chemical Society, 2014, 118 (24), pp.6456-6465. ⟨10.1021/jp411671a⟩. ⟨hal-02126799⟩
  • R. Chaudret, B. De Courcy, J. Contreras-García, Eric Gloaguen, A. Zehnacker-Rentien, et al.. Unraveling non-covalent interactions within flexible biomolecules: from electron density topology to gas phase spectroscopy. Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2014, 16, pp.9876-9891. ⟨10.1039/C3CP52774C⟩. ⟨hal-01131254⟩
  • Isabelle Demachy, Jean-Philip Piquemal. La surface d'énergie potentielle vue par les champs de forces. L'Actualité Chimique, Société chimique de France, 2014, 388-389, pp.37-42. ⟨hal-00960389⟩
  • Nohad Gresh, Krystel El Hage, David Perahia, Jean-Philip Piquemal, Catherine Berthomieu, et al.. Polarizable Molecular Mechanics Studies of Cu(I)/Zn(II) Superoxide Dismutase: Bimetallic Binding Site and Structured Waters. Journal of Computational Chemistry, Wiley, 2014, 35 (29), pp.2096-2106. ⟨10.1002/jcc.23724⟩. ⟨hal-01081843⟩
  • R. Chaudret, N. Gresh, C. Narth, L. Lagardere, T. A. Darden, et al.. 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. Journal of Physical Chemistry A, American Chemical Society, 2014, 118 (35), pp.7598-7612. ⟨10.1021/jp5051657⟩. ⟨hal-01287208⟩
  • Filippo Lipparini, Louis Lagardère, Giovanni Scalmani, Benjamin Stamm, Eric Cancès, et al.. Quantum Calculations in Solution for Large to Very Large Molecules: A New Linear Scaling QM/Continuum Approach. Journal of Physical Chemistry Letters, American Chemical Society, 2014, 5, pp.953-958. ⟨10.1021/jz5002506⟩. ⟨hal-00956401⟩
  • Filippo Lipparini, Giovanni Scalmani, Louis Lagardère, Benjamin Stamm, Eric Cancès, et al.. Quantum, classical, and hybrid QM/MM calculations in solution: General implementation of the ddCOSMO linear scaling strategy. Journal of Chemical Physics, American Institute of Physics, 2014, 141 (18), pp.184108. ⟨10.1063/1.4901304⟩. ⟨hal-01090954⟩
  • Filippo Lipparini, Louis Lagardère, Benjamin Stamm, Eric Cancès, Michael Schnieders, et al.. Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations. Journal of Chemical Theory and Computation, American Chemical Society, 2014, 10 (4), pp.1638-1651. ⟨10.1021/ct401096t⟩. ⟨hal-01090942⟩
  • David Guenther, Roberto Alvarez-Boto, Julia Contreras-Garcia, Jean-Philip Piquemal, Julien Tierny. Characterizing Molecular Interactions in Chemical Systems. IEEE Transactions on Visualization and Computer Graphics, Institute of Electrical and Electronics Engineers, 2014, 20 (12), pp.2476-2485. ⟨10.1109/TVCG.2014.2346403⟩. ⟨hal-01146475⟩
  • Robin Chaudret, Julia Contreras-García, Mickaël Delcey, Olivier Parisel, Weitao Yang, et al.. Revisiting H2O Nucleation around Au + and Hg 2+ : The Peculiar “Pseudo-Soft” Character of the Gold Cation. Journal of Chemical Theory and Computation, American Chemical Society, 2014, 10 (5), pp.1900-1909. ⟨10.1021/ct4006135⟩. ⟨hal-02126798⟩
  • R. Duke, O. Starovoytov, J.-P. Piquemal, G. A. Cisneros. GEM*: A Molecular Electronic Density--Based Force Field for Classical Molecular Dynamics Simulations . Journal of Chemical Theory and Computation, American Chemical Society, 2014, 10, pp.1361-1365. ⟨10.1021/ct500050p⟩. ⟨hal-01287209⟩
  • Aude Marjolin, Christophe Gourlaouen, Carine Clavaguéra, Pengyu Y. Ren, Jean-Philip Piquemal, et al.. Hydration gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics. Journal of Molecular Modeling, Springer Verlag (Germany), 2014, 20, pp.2471. ⟨10.1007/s00894-014-2471-6⟩. ⟨hal-01157657⟩
  • Dong Fang, Jean-Philip Piquemal, Shubin Liu, G. Andrés Cisneros. DFT-steric-based energy decomposition analysis of intermolecular interactions. Theoretical Chemistry Accounts: Theory, Computation, and Modeling, Springer Verlag, 2014, 133 (5), ⟨10.1007/s00214-014-1484-7⟩. ⟨hal-02126797⟩
  • Elodie Goldwaser, Benoit de Courcy, Luc Demange, Christiane Garbay, Françoise Raynaud, et al.. 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. Journal of Molecular Modeling, Springer Verlag (Germany), 2014, 20 (11), ⟨10.1007/s00894-014-2472-5⟩. ⟨hal-02126794⟩
  • Wang-Qing Liu, Valentino Megale, Lucia Borriello, Bertrand Leforban, Matthieu Montes, et al.. Synthesis and structure–activity relationship of non-peptidic antagonists of neuropilin-1 receptor. Bioorganic and Medicinal Chemistry Letters, Elsevier, 2014, 24 (17), pp.4254-4259. ⟨10.1016/j.bmcl.2014.07.028⟩. ⟨hal-02126861⟩
  • Mike Devereux, Nohad Gresh, Jean-Philip Piquemal, Markus Meuwly. A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field. Journal of Computational Chemistry, Wiley, 2014, 35 (21), pp.1577-1591. ⟨10.1002/jcc.23661⟩. ⟨hal-02126862⟩
  • Krystel El Hage, Jean-Philip Piquemal, Zeina Hobaika, Richard Maroun, Nohad Gresh. 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. Journal of Physical Chemistry A, American Chemical Society, 2014, 118 (41), pp.9772-9782. ⟨10.1021/jp5079899⟩. ⟨hal-02126859⟩
  • Robin Chaudret, Nohad Gresh, Andrés Cisneros, Anthony Scemama, Jean-Philip Piquemal. Further refinements of next-generation force fields -- Nonempirical localization of off-centered points in molecules. Canadian Journal of Chemistry, NRC Research Press, 2013, 91 (9), pp.804-810. ⟨10.1139/cjc-2012-0547⟩. ⟨hal-00875425⟩
  • Christophe Gourlaouen, Carine Clavaguéra, Aude Marjolin, Jean-Philip Piquemal, Jean-Pierre Dognon. Understanding the structure and electronic properties of Th4+-water complexes. Canadian Journal of Chemistry, NRC Research Press, 2013, 91 (9), pp.821-831. ⟨10.1139/cjc-2012-0546⟩. ⟨hal-00926680⟩
  • A. Marjolin, C. Gourlaouen, Carine Clavaguéra, J. -P. Dognon, J. -P. Piquemal. Towards energy decomposition analysis for open and closed shell f-elements mono aqua complexes. Chemical Physics Letters, Elsevier, 2013, 563, pp.25-29. ⟨10.1016/j.cplett.2013.01.066⟩. ⟨hal-00880177⟩
  • Joseph Lane, Julia Contreras-García, Jean-Philip Piquemal, Benjamin Miller, Henrik Kjaergaard. Are Bond Critical Points Really Critical for Hydrogen Bonding?. Journal of Chemical Theory and Computation, American Chemical Society, 2013, 9 (8), pp.3263-3266. ⟨10.1021/ct400420r⟩. ⟨hal-02126863⟩
  • Dong Fang, Robin Chaudret, Jean-Philip Piquemal, G. Andrés Cisneros. Toward a Deeper Understanding of Enzyme Reactions Using the Coupled ELF/NCI Analysis: Application to DNA Repair Enzymes. Journal of Chemical Theory and Computation, American Chemical Society, 2013, 9 (5), pp.2156-2160. ⟨10.1021/ct400130b⟩. ⟨hal-02126800⟩
  • Marie-Céline van Severen, Ulf Ryde, Olivier Parisel, Jean-Philip Piquemal. Understanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins. Journal of Chemical Theory and Computation, American Chemical Society, 2013, 9 (5), pp.2416-2424. ⟨10.1021/ct300524v⟩. ⟨hal-02126839⟩
  • Krystel El Hage, Jean-Philip Piquemal, Zeina Hobaika, Richard Maroun, Nohad Gresh. Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds?. Journal of Computational Chemistry, Wiley, 2013, 34 (13), pp.1125-1135. ⟨10.1002/jcc.23242⟩. ⟨hal-02126864⟩
  • Natacha Gillet, Robin Chaudret, Julia Contreras-Garcı́a, Weitao Yang, Bernard Silvi, et al.. Coupling Quantum Interpretative Techniques: Another Look at Chemical Mechanisms in Organic Reactions. Journal of Chemical Theory and Computation, American Chemical Society, 2012, 8 (11), pp.3993-3997. ⟨10.1021/ct300234g⟩. ⟨hal-02126838⟩
  • Jean-Philip Piquemal, Kenneth Jordan. From quantum mechanics to force fields: new methodologies for the classical simulation of complex systems. Theoretical Chemistry Accounts: Theory, Computation, and Modeling, Springer Verlag, 2012, 131 (4), ⟨10.1007/s00214-012-1207-x⟩. ⟨hal-02127244⟩
  • Marie-Céline van Severen, Robin Chaudret, Olivier Parisel, Jean-Philip Piquemal. Toward a ligand specific of Pb2+ with respect to the Zn2+ and Ca2+ cations: A track from quantum chemistry. Chemical Physics Letters, Elsevier, 2012, 532, pp.9-12. ⟨10.1016/j.cplett.2012.02.037⟩. ⟨hal-02126868⟩
  • Julia Contreras-García, Monica Calatayud, Jean-Philip Piquemal, J.M. Recio. Ionic interactions: Comparative topological approach. Computational and Theoretical Chemistry, Elsevier, 2012, 998, pp.193-201. ⟨10.1016/j.comptc.2012.07.043⟩. ⟨hal-02126866⟩
  • Jiajing Zhang, Wei Yang, Jean-Philip Piquemal, Pengyu Ren. Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential. Journal of Chemical Theory and Computation, American Chemical Society, 2012, 8 (4), pp.1314-1324. ⟨10.1021/ct200812y⟩. ⟨hal-02126837⟩
  • A. Marjolin, C. Gourlaouen, Carine Clavaguéra, P.Y. Ren, J.C. Wu, et al.. Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: From gas-phase energetics to hydration free energies. Theoretical Chemistry Accounts: Theory, Computation, and Modeling, Springer Verlag, 2012, 131 (March), pp.1198. ⟨10.1007/s00214-012-1198-7⟩. ⟨hal-00904389⟩
  • Céline Roux, Forum Bhatt, Johanna Foret, Benoit de Courcy, Nohad Gresh, et al.. The reaction mechanism of type I phosphomannose isomerases: New information from inhibition and polarizable molecular mechanics studies. Proteins - Structure, Function and Bioinformatics, Wiley, 2011, 79 (1), pp.203-220. ⟨10.1002/prot.22873⟩. ⟨hal-02126875⟩
  • Aurelien de la Lande, Dennis R Salahub, Jacques Maddaluno, Anthony Scemama, Julien Pilme, et al.. Spin-driven activation of dioxygen in various metalloenzymes and their inspired models.. Journal of Computational Chemistry, Wiley, 2011, 32 (6), pp.1178-1182. ⟨10.1002/jcc.21698⟩. ⟨hal-00992047⟩
  • Nohad Gresh, Benoit de Courcy, Jean-Philip Piquemal, Johanna Foret, Stéphanie Courtiol-Legourd, et al.. Polarizable Water Networks in Ligand–Metalloprotein Recognition. Impact on the Relative Complexation Energies of Zn-Dependent Phosphomannose Isomerase with d -Mannose 6-Phosphate Surrogates. Journal of Physical Chemistry B, American Chemical Society, 2011, 115 (25), pp.8304-8316. ⟨10.1021/jp2024654⟩. ⟨hal-02126871⟩
  • Lauréline Bonniard, Aurelien de la Lande, Simon Ulmer, Jean-Philip Piquemal, Olivier Parisel, et al.. Competitive ligand/chelate binding in [Cu(TMPA)]+ and [Cu(tren)]+ based complexes. Catalysis Today, Elsevier, 2011, 177 (1), pp.79-86. ⟨10.1016/j.cattod.2011.07.015⟩. ⟨hal-02126870⟩
  • Robin Chaudret, Nohad Gresh, Olivier Parisel, Jean-Philip Piquemal. Many-body exchange-repulsion in polarizable molecular mechanics. I. orbital-based approximations and applications to hydrated metal cation complexes. Journal of Computational Chemistry, Wiley, 2011, 32 (14), pp.2949-2957. ⟨10.1002/jcc.21865⟩. ⟨hal-02126872⟩
  • Robin Chaudret, Jean-Philip Piquemal, G. Andrés Cisneros. Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations. Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2011, 13 (23), pp.11239. ⟨10.1039/c0cp02550j⟩. ⟨hal-02126836⟩
  • Julia Contreras-García, Erin Johnson, Shahar Keinan, Robin Chaudret, Jean-Philip Piquemal, et al.. NCIPLOT: A Program for Plotting Noncovalent Interaction Regions. Journal of Chemical Theory and Computation, American Chemical Society, 2011, 7 (3), pp.625-632. ⟨10.1021/ct100641a⟩. ⟨hal-02126834⟩
  • M.-C. van Severen, J.-P. Piquemal, O. Parisel. Enforcing hemidirectionality in Pb(II) complexes: The importance of anionic ligands. Chemical Physics Letters, Elsevier, 2011, 510 (1-3), pp.27-30. ⟨10.1016/j.cplett.2011.04.096⟩. ⟨hal-02126869⟩
  • Robin Chaudret, G. Andrés Cisneros, Olivier Parisel, Jean-Philip Piquemal. Unraveling Low-Barrier Hydrogen Bonds in Complex Systems with a Simple Quantum Topological Criterion. Chemistry - A European Journal, Wiley-VCH Verlag, 2011, 17 (10), pp.2833-2837. ⟨10.1002/chem.201002978⟩. ⟨hal-02126873⟩
  • Anthony Scemama, Michel Caffarel, Robin Chaudret, Jean-Philip Piquemal. Electron Pair Localization Function (EPLF) for Density Functional Theory and ab Initio Wave Function-Based Methods: A New Tool for Chemical Interpretation. Journal of Chemical Theory and Computation, American Chemical Society, 2011, 7 (3), pp.618-624. ⟨10.1021/ct1005938⟩. ⟨hal-00874618⟩
  • Benoit de Courcy, Jean-Pierre Dognon, Carine Clavaguéra, Nohad Gresh, Jean-Philip Piquemal. Interactions within the alcohol dehydrogenase Zn(II)-metalloenzyme active site: Interplay between subvalence, electron correlation/dispersion, and charge transfer/induction effects. International Journal of Quantum Chemistry, Wiley, 2011, 111 (6), pp.1213-1221. ⟨10.1002/qua.22760⟩. ⟨hal-00926669⟩
  • A. de la Lande, J. Maddaluno, O. Parisel, A. Darden, J. Piquemal. 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. INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 2010, 2 (1), pp.3-11. ⟨10.1007/s12539-010-0096-8⟩. ⟨hal-02126831⟩
  • Eric Gloaguen, B. de Courcy, J.-P. Piquemal, J. Pilmé, O. Parisel, et al.. Gas-phase folding of a two-residue model peptide chain: on the importance of an interplay between experiment and theory.. Journal of the American Chemical Society, American Chemical Society, 2010, 132 (34), pp.11860-3. ⟨10.1021/ja103996q⟩. ⟨hal-00915204⟩
  • Mike Devereux, Marie-Céline van Severen, Olivier Parisel, Jean-Philip Piquemal, Nohad Gresh. 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. Journal of Chemical Theory and Computation, American Chemical Society, 2010, 7 (1), pp.138-147. ⟨10.1021/ct1004005⟩. ⟨hal-02126874⟩
  • Jean-Philip Piquemal, Dennis Salahub. Editorial: Special issue on quantum mechanical modeling of biological systems. INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 2010, 2 (1), pp.1-2. ⟨10.1007/s12539-010-0001-5⟩. ⟨hal-02127241⟩
  • Nohad Gresh, N. Audiffren, J.-P. Piquemal, J. de Ruyck, M. Ledecq, et al.. 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.. Journal of Physical Chemistry B, American Chemical Society, 2010, pp.4884. ⟨hal-00494595⟩
  • B. de Courcy, J. P. Piquemal, C. Garbay, N. Gresh. Polarizable water molecules in ligand-macromolecule recognition. Impact on the relative affinities of competing pyrrolopyrimidine inhibitors for FAK kinase.. Journal of the American Chemical Society, American Chemical Society, 2010, 132, pp.3312. ⟨hal-00494585⟩
  • C. Gourlaouen, O. Parisel, J.-P. Piquemal. Importance of backdonation in [M–(CO)]p+ complexes isoelectronic to [Au–(CO)]+. Journal of Chemical Physics, American Institute of Physics, 2010, 133 (12), pp.124310. ⟨10.1063/1.3491266⟩. ⟨hal-02126876⟩
  • M.-C. van Severen, J.-P. Piquemal, O. Parisel. Lead Substitution in Synaptotagmin: A Case Study. Journal of Physical Chemistry B, American Chemical Society, 2010, 114 (11), pp.4005-4009. ⟨10.1021/jp910131r⟩. ⟨hal-02126877⟩
  • B. de Courcy, L. G. Pedersen, O. Parisel, N. Gresh, B. Silvi, et al.. 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.. Journal of Chemical Theory and Computation, American Chemical Society, 2010, 6 (4), pp.1048-1063. ⟨10.1021/ct100089s⟩. ⟨hal-00996393⟩
  • Johnny Wu, Jean-Philip Piquemal, Robin Chaudret, Peter Reinhardt, Pengyu Ren. Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field. Journal of Chemical Theory and Computation, American Chemical Society, 2010, 6 (7), pp.2059-2070. ⟨10.1021/ct100091j⟩. ⟨hal-02126833⟩
  • Johanna Foret, Benoit de Courcy, Nohad Gresh, Jean-Philip Piquemal, Laurent Salmon. 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. Bioorganic and Medicinal Chemistry, Elsevier, 2009, 17 (20), pp.7100-7107. ⟨10.1016/j.bmc.2009.09.005⟩. ⟨hal-02126828⟩
  • Dennis Elking, G. Andrés Cisneros, Jean-Philip Piquemal, Thomas Darden, Lee Pedersen. Gaussian Multipole Model (GMM). Journal of Chemical Theory and Computation, American Chemical Society, 2009, 6 (1), pp.190-202. ⟨10.1021/ct900348b⟩. ⟨hal-02126830⟩
  • Aurélien de la Lande, Dennis Salahub, Vicent Moliner, Hélène Gérard, Jean-Philip Piquemal, et al.. Dioxygen Activation by Mononuclear Copper Enzymes: Insights from a Tripodal Ligand Mimicking Their Cu M Coordination Sphere. Inorganic Chemistry, American Chemical Society, 2009, 48 (15), pp.7003-7005. ⟨10.1021/ic900567z⟩. ⟨hal-02126825⟩
  • R. Chaudret, S. Ulmer, M.-C. van Severen, N. Gresh, O. Parisel, et al.. Progress Towards Accurate Molecular Modeling of Metal Complexes Using Polarizable Force Fields. AIP Conference Proceedings, American Institute of Physics, 2009, 1102, pp.185-192. ⟨10.1063/1.3108373⟩. ⟨hal-02126821⟩
  • C. Gourlaouen, O. Parisel, J.-P. Piquemal. Trends in ns2np0 [M(CO)]q+ complexes: From germanium to element 114 (Uuq). Chemical Physics Letters, Elsevier, 2009, 469 (1-3), pp.38-42. ⟨10.1016/j.cplett.2008.12.040⟩. ⟨hal-02126822⟩
  • P. Reinhardt, J-P. Piquemal. New intermolecular benchmark calculations on the water dimer: SAPT and supermolecular post-Hartree-Fock approaches. International Journal of Quantum Chemistry, Wiley, 2009, 109 (14), pp.3259-3267. ⟨10.1002/qua.22299⟩. ⟨hal-02126824⟩
  • B. de Courcy, N. Gresh, J.-P. Piquemal. 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. INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 2009, 1 (1), pp.55-60. ⟨10.1007/s12539-008-0027-0⟩. ⟨hal-02126823⟩
  • M. van Severen, J.-P. Piquemal, O. Parisel. Beyond holo/hemidirectionality in Pb(II) complexes: Can the valence lone pair be bisdirected?. Chemical Physics Letters, Elsevier, 2009, 478 (1-3), pp.17-19. ⟨10.1016/j.cplett.2009.07.036⟩. ⟨hal-02126826⟩
  • Christophe Gourlaouen, Hélène Gérard, Jean-Philip Piquemal, Olivier Parisel. Understanding Lead Chemistry from Topological Insights: The Transition between Holo- and Hemidirected Structures within the [Pb(CO)n]2+ Model Series. Chemistry - A European Journal, Wiley-VCH Verlag, 2008, 14 (9), pp.2730-2743. ⟨10.1002/chem.200701265⟩. ⟨hal-02126879⟩
  • G. Cisneros, S. Na-Im Tholander, O. Parisel, T. Darden, D. Elking, et al.. Simple formulas for improved point-charge electrostatics in classical force fields and hybrid quantum mechanical/molecular mechanical embedding. International Journal of Quantum Chemistry, Wiley, 2008, 108 (11), pp.1905-1912. ⟨10.1002/qua.21675⟩. ⟨hal-02126814⟩
  • J.-P. Piquemal, J. Pilmé, O. Parisel, H. Gerard, I. Fourré, et al.. What can be learnt on biologically relevant systems from the topological analysis of the electron localization function?. International Journal of Quantum Chemistry, Wiley, 2008, 108 (11), pp.1951-1969. ⟨10.1002/qua.21711⟩. ⟨hal-02126817⟩
  • Benoit de Courcy, Jean-Philip Piquemal, Nohad Gresh. Energy Analysis of Zn Polycoordination in a Metalloprotein Environment and of the Role of a Neighboring Aromatic Residue. What Is the Impact of Polarization?. Journal of Chemical Theory and Computation, American Chemical Society, 2008, 4 (10), pp.1659-1668. ⟨10.1021/ct800200j⟩. ⟨hal-02126819⟩
  • Peter Reinhardt, Jean-Philip Piquemal, Andreas Savin. Fragment-Localized Kohn−Sham Orbitals via a Singles Configuration-Interaction Procedure and Application to Local Properties and Intermolecular Energy Decomposition Analysis. Journal of Chemical Theory and Computation, American Chemical Society, 2008, 4 (12), pp.2020-2029. ⟨10.1021/ct800242n⟩. ⟨hal-02126818⟩
  • Julien Pilmé, Jean-Philip Piquemal. Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments. Journal of Computational Chemistry, Wiley, 2008, 29 (9), pp.1440-1449. ⟨10.1002/jcc.20904⟩. ⟨hal-02126878⟩
  • Céline Roux, Nohad Gresh, Lalith Perera, Jean-Philip Piquemal, Laurent Salmon. 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. Journal of Computational Chemistry, Wiley, 2007, 28 (5), pp.938-957. ⟨10.1002/jcc.20586⟩. ⟨hal-02126881⟩
  • Nohad Gresh, Clément Roux, N. Gresh, L. E. Perera, J.-P. Piquemal, et al.. 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.. Journal of Computational Chemistry, Wiley, 2007, 28, pp.938. ⟨hal-00494629⟩
  • Nohad Gresh, G. Andres Cisneros, T.A. Darden, J.-P. Piquemal. Anisotropic, polarizable molecular mechanics studies of inter-, intramolecular interactions, and ligand-macromolecule complexes.A bottom-up strategy. Journal of Chemical Theory and Computation, American Chemical Society, 2007, pp.1960. ⟨hal-00494588⟩
  • Jean-Philip Piquemal, Riccardo Chelli, Piero Procacci, Nohad Gresh. Key Role of the Polarization Anisotropy of Water in Modeling Classical Polarizable Force Fields. Journal of Physical Chemistry A, American Chemical Society, 2007, 111 (33), pp.8170-8176. ⟨10.1021/jp072687g⟩. ⟨hal-02126880⟩
  • L. M Miller Jenkins, T. Hara, S. R Durell, R. Hayashi, J. K Inman, et al.. The specificity of acyl transfer from 2-mercaptobenzamide thioesters to the HIV-1 nucleocapsid protein. ]. Journal of the American Chemical Society, American Chemical Society, 2007, pp.11067. ⟨hal-00494580⟩
  • Jean-Philip Piquemal, Hilaire Chevreau, Nohad Gresh. Toward a Separate Reproduction of the Contributions to the Hartree−Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential. Journal of Chemical Theory and Computation, American Chemical Society, 2007, 3 (3), pp.824-837. ⟨10.1021/ct7000182⟩. ⟨hal-02126810⟩
  • G. Andrés Cisneros, Dennis Elking, Jean-Philip Piquemal, Thomas Darden. Numerical Fitting of Molecular Properties to Hermite Gaussians. Journal of Physical Chemistry A, American Chemical Society, 2007, 111 (47), pp.12049-12056. ⟨10.1021/jp074817r⟩. ⟨hal-02126812⟩
  • G. Andrés Cisneros, Jean-Philip Piquemal, Thomas Darden. Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods. Journal of Chemical Physics, American Institute of Physics, 2006, 125 (18), pp.184101. ⟨10.1063/1.2363374⟩. ⟨hal-02126808⟩
  • Christophe Gourlaouen, Jean-Philip Piquemal, Olivier Parisel. [Pb(H2O)]2+ and [Pb(OH)]+: Four-component density functional theory calculations, correlated scalar relativistic constrained-space orbital variation energy decompositions, and topological analysis. Journal of Chemical Physics, American Institute of Physics, 2006, 124 (17), pp.174311. ⟨10.1063/1.2186994⟩. ⟨hal-02127222⟩
  • Christophe Gourlaouen, Jean-Philip Piquemal, Trond Saue, Olivier Parisel. 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+). Journal of Computational Chemistry, Wiley, 2006, 27 (2), pp.142-156. ⟨10.1002/jcc.20329⟩. ⟨hal-02127159⟩
  • Nohad Gresh, J.-P. Piquemal, G. Andres Cisneros, P. Reinhardt, T.A. Darden. Towards a force field based on density fitting. Journal of Chemical Physics, American Institute of Physics, 2006, 124, pp.104101. ⟨hal-00494627⟩
  • Jean-Philip Piquemal, Lalith Perera, G. Andrés Cisneros, Pengyu Ren, Lee Pedersen, et al.. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. Journal of Chemical Physics, American Institute of Physics, 2006, 125 (5), pp.054511. ⟨10.1063/1.2234774⟩. ⟨hal-02126806⟩
  • G. Andrés Cisneros, Jean-Philip Piquemal, Thomas Darden. Quantum Mechanics/Molecular Mechanics Electrostatic Embedding with Continuous and Discrete Functions. Journal of Physical Chemistry B, American Chemical Society, 2006, 110 (28), pp.13682-13684. ⟨10.1021/jp062768x⟩. ⟨hal-02126805⟩
  • Jean-Philip Piquemal, Julien Pilmé. Comments on the nature of the bonding in oxygenated dinuclear copper enzyme models. Journal of Molecular Structure: THEOCHEM, Elsevier, 2006, 764 (1-3), pp.77 - 86. ⟨10.1016/j.theochem.2006.02.013⟩. ⟨hal-01906896⟩
  • G. Andrés Cisneros, Jean-Philip Piquemal, Thomas Darden. Intermolecular electrostatic energies using density fitting. Journal of Chemical Physics, American Institute of Physics, 2005, 123 (4), pp.044109. ⟨10.1063/1.1947192⟩. ⟨hal-02126804⟩
  • Nohad Gresh, Jean-Philip Piquemal, Morris Krauss. Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations. Journal of Computational Chemistry, Wiley, 2005, 26 (11), pp.1113-1130. ⟨10.1002/jcc.20244⟩. ⟨hal-02127150⟩
  • Jean-Philip Piquemal, Antonio Marquez, Olivier Parisel, Claude Giessner-Prettre. A CSOV study of the difference between HF and DFT intermolecular interaction energy values: The importance of the charge transfer contribution. Journal of Computational Chemistry, Wiley, 2005, 26 (10), pp.1052-1062. ⟨10.1002/jcc.20242⟩. ⟨hal-02126803⟩
  • Jens Antony, Jean-Philip Piquemal, Nohad Gresh. Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-β-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry. Journal of Computational Chemistry, Wiley, 2005, 26 (11), pp.1131-1147. ⟨10.1002/jcc.20245⟩. ⟨hal-02127145⟩
  • Jean-Philip Piquemal, Nohad Gresh, Claude Giessner-Prettre. Improved Formulas for the Calculation of the Electrostatic Contribution to the Intermolecular Interaction Energy from Multipolar Expansion of the Electronic Distribution. Journal of Physical Chemistry A, American Chemical Society, 2003, 107 (48), pp.10353-10359. ⟨10.1021/jp035748t⟩. ⟨hal-02126882⟩
  • Jean-Philip Piquemal, Ben Williams-Hubbard, Natalie Fey, Robert Deeth, Nohad Gresh, et al.. Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF. Journal of Computational Chemistry, Wiley, 2003, 24 (16), pp.1963-1970. ⟨10.1002/jcc.10354⟩. ⟨hal-02127138⟩
  • Jean-Philip Piquemal, Jacques Maddaluno, Bernard Silvi, Claude Giessner-Prettre. Theoretical study of phenol and 2-aminophenol docking at a model of the tyrosinase active site. New Journal of Chemistry, Royal Society of Chemistry, 2003, 27 (6), pp.909-913. ⟨10.1039/B210307A⟩. ⟨hal-02126801⟩

Conference papers2 documents

  • R. Chaudret, B. de Courcy, A. Marjolin, M.-C. van Severen, P. Ren, et al.. Unraveling interactions in large complex systems using quantum chemistry interpretative techniques and new generation polarizable force fields. INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2009: (ICCMSE 2009), 2009, Rhodes, Greece. pp.699-702. ⟨hal-02126865⟩
  • J. Piquemal, S. Chamayou, Isabelle Nadaud, Michel Beckert, Catherine Lapierre, et al.. Modulation of caffeic acid O-methyltransferase (COMT) in maize. 9. International cell wall Meeting, Sep 2001, Toulouse, France. ⟨hal-01190917⟩

Book sections5 documents

  • Jean-Philip Piquemal, G. Andrés Cisneros. Status of the Gaussian Electrostatic Model, a Density-Based Polarizable Force Field. Qiang Cui, Pengyu Ren and Markus Meuwly. Many-body effects and electrostatics, Pan Standford Publishing, pp.269-299, 2016, multi-scale computations of Biomolecules, 9789814613927. ⟨10.1201/b21343-11⟩. ⟨hal-01114075⟩
  • Christophe Narth, Zeina Maroun, Roberto A. Boto, Robin Chaudret, Marie-Laure Bonnet, et al.. A complete NCI perspective: from new bonds to reactivity. 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⟩. ⟨hal-01224203⟩
  • Nohad Gresh, Krystel El Hage, Elodie Goldwaser, Benoit De Courcy, Robin Chaudret, et al.. Addressing the issues of non-isotropy and non-additivity in the development of quantum chemistry-grounded polarizable molecular mechanics.. 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⟩. ⟨hal-01104542⟩
  • Yue Shi, Pengyu Ren, Michael Schnieders, Jean-Philip Piquemal. Polarizable Force Fields for Biomolecular Modeling. Reviews in Computational Chemistry, 28 (51), Wiley, 2015, ⟨10.1002/9781118889886.ch2⟩. ⟨hal-01114184⟩
  • G.A. Cisneros, T.A. Darden, N. Gresh, J. Pilme, P. Reinhardt, et al.. Design Of Next Generation Force Fields From AB Initio Computations: Beyond Point Charges Electrostatics. Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications, Springer Netherlands, pp.137-172, 2009. ⟨hal-02127328⟩