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Jean-Philip Piquemal

CV de Jean-Philip Piquemal
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Affiliations actuelles
  • 413221
  • 454935
Identifiants chercheurs
  • IdHAL jean-philip-piquemal
  • ResearcherId : B-9901-2009
  • ORCID 0000-0001-6615-9426
  • Google Scholar : https://scholar.google.fr/citations?user=z0cOrb0AAAAJ&hl=fr
  • IdRef : 089289439
  • ResearcherId : http://www.researcherid.com/rid/B-9901-2009
Contact
Site web
  • https://piquemalresearch.com/
  • https://mastodon-pa.sorbonne-universite.fr/@piquemal

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; Twitter: [@jppiquem](https://twitter.com/jppiquem) (personal); [@piquemalgroup](https://twitter.com/PiquemalGroup) (research team) Mastodon: [@piquemal@mastodon-pa.sorbonne-universite.fr](https://mastodon-pa.sorbonne-universite.fr/@piquemal) LinkedIn: [@jppiquem](https://www.linkedin.com/in/jppiquem/) **Research Interests:** * Computational Quantum Chemistry; * Molecular Simulation; * Computational Drug Discovery; * Computer Science including High Performance Computing, Quantum Computing and Machine Learning. **Present Position** * Distinguished Professor (EXceptional class, PREX2) of Theoretical Chemistry, [Sorbonne Université](http://www.sorbonne-universite.fr/) (Paris, France); * Director of the [Laboratoire de Chimie Théorique, UMR 7616 Sorbonne Université & CNRS, Department of Chemistry;](http://www.lct.jussieu.fr) * Principal Investigator, [EMC2 (Extreme-scale Mathematically-based Computational Chemistry)](https://erc-emc2.eu/) ERC SyG project; * Research Adjunct Professor, [Department of Biomedical Engineering](https://www.bme.utexas.edu/), The University of Texas at Austin (USA); * Editor, [Results in Chemistry](https://www.journals.elsevier.com/results-in-chemistry) (Elsevier). **Updated Publication List and Bibliometrics :** See my [Google scholar profil](https://scholar.google.com/citations?user=z0cOrb0AAAAJ&hl=fr) or visit my webpage : [http://piquemalresearch.com/publications/](http://piquemalresearch.com/publications/ "Jean-Philip Piquemal publications") **Software development** My research team and I lead the development of the Tinker-HP molecular dynamics package ([https://tinker-hp.org](https://tinker-hp.org "Tinker-HP")) dedicated to new generation potentials (polarizable force fields and neural networks). **Professional Background** * 2023-present : Distinguished Professor (Exceptional class, PREX2), CNU section 31, SU. * 2020-present : Co-founder (2020) and CSO of [Qubit Pharmaceuticals](https://www.qubit-pharmaceuticals.com/) * 2019-present : Director [Laboratoire de Chimie Théorique (LCT)](http://www.lct.jussieu.fr), Department of Chemistry, SU & CNRS * 2019-present : Team leader: Extreme-scale Mathematically-based Computational Chemistry (EMC2), [LCT](http://www.lct.jussieu.fr), SU/CNRS. * 2019-present : PI of the [EMC2 ERC Synergy project](https://erc-emc2.eu/) (2019-2025) * 2015-present : Research Adjunct Professor, [Department of Biomedical Engineering](https://www.bme.utexas.edu/), The University of Texas at Austin (USA). * 2020-2023 : Member of the [PRACE](https://prace-ri.eu/) Steering Commitee (Partnership for Advanced Computing in Europe). * 2019-2023 : Distinguished Professor (Exceptional class, PREX1), CNU section 31, SU. * 2016-2021 : Junior Member of the [Institut Universitaire de France](https://www.iufrance.fr/) (research chair) * 2016-2019 : Full Professor (first class, PR1), CNU section 31, SU. * 2012-2019 : Team leader of the MC2 interdisciplinary project team at [ISCD](http://iscd.upmc.fr/) (Institute for Computations and data), SU. * 2012-2018 : Director of the Institut Parisien de Chimie Physique et Théorique ([IP2CT](http://www.ip2ct.upmc.fr/)), 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, PR2), UPMC. * 2009-2011 : Associate Professor (Maître de Conférences - HDR), UPMC * 2006-2009 : Assistant Professor (Maître de Conférences), UPMC. * 2004-2006 : NIH Postdoctoral Visiting Fellow, [NIEHS](https://www.niehs.nih.gov), Research Triangle Park, NC, USA (group of Thomas Darden). **Education** * 2009 : Research Habilitation (HDR) in Theoretical Chemistry, UPMC. * 2004 : Ph.D. Thesis in Theoretical Chemistry, Laboratoire de Chimie Théorique, UPMC. \[[Academic Genealogy](https://academictree.org/chemistry/tree.php?pid=70959)\] * 2001 : Diplôme d'Etude Approfondie (DEA) in Computational and Theoretical Chemistry (DEA National CIT), UPMC. * 2000 : Master degree (Maîtrise) in Chemistry (major: Physical Chemistry), 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 **Teaching** Theoretical Chemistry (Quantum chemistry and Molecular Simulation), Physical Chemistry, Machine Learning, Computer Science and Programming. **Selected Honors & Awards** * 2022: [HPC Innovation Excellence Award](https://www.hpcwire.com/off-the-wire/hyperion-research-announces-winners-of-hpc-innovation-excellence-awards/) . * 2022: H2020 Innovative Training Networks (ITN), Co-PI of the [PHYMOL](http://www.phymol.eu/) project (Marie Skłodowska–Curie Actions Doctoral Network on Intermolecular Interactions). * 2022: Fellow of the [Royal Society of Chemistry](https://www.rsc.org/) (FSRC, UK) * 2022: Nominated as part of the [100 french innovators of the year](https://www.lepoint.fr/sciences-nature/les-meilleurs-inventeurs-francais-sont-09-06-2022-2478893_1924.php) by the french newspaper Le Point * 2022: [i-Nov](https://www.enseignementsup-recherche.gouv.fr/fr/le-concours-i-nov-49817) innovation award (BPI France/MESRI) * 2021: [EIC-Accelerator](https://eic.ec.europa.eu/eic-funding-opportunities/eic-accelerator_en) innovation program (European Research Council) * 2020: [i-Lab](https://www.enseignementsup-recherche.gouv.fr/fr/le-concours-i-lab-49808) innovation award (BPI France/MESRI) * 2018: [ERC Synergy](https://erc.europa.eu/funding/synergy-grants), Principal Investigator, project Extreme-scale Mathematically-based Computational Chemistry (EMC2 with E. Cancès, L. Grigori and Y. Maday) * 2018: [Atos Joseph Fourier Prize](https://fr.wikipedia.org/wiki/Prix_Atos_-_Joseph_Fourier) in Numerical Simulation (1st prize) * 2018: [France-Berkeley Fund](https://fbf.berkeley.edu/) Award * 2016: Nominated as a Junior Member of the [Institut Universitaire de France](https://en.wikipedia.org/wiki/Institut_Universitaire_de_France) (junior chair 2016-2021) * 2012: Emergence-UPMC fund Award * 2011: [Wiley-International Journal of Quantum Chemistry Young Investigator Award](https://sanibelsymposium.qtp.ufl.edu/awards-poster-sizes/winners/) * 2008: [France-Canada Research Fund](https://francecanadaculture.org/france-canada-research-fund/) Award * 2004: National Institute of Health (NIH) Postdoctoral Visiting Fellowship (2004-2006) * 2001: PhD scholarship from the Ministry of Higher Education, Research and Innovation (MESRI; 2001-2004) **Industry** * Co-founder (2020) and CSO of [Qubit Pharmaceuticals](https://qubit-pharmaceuticals.com/) **Editorial Activites** * Editor: [Results in Chemistry](https://www.journals.elsevier.com/results-in-chemistry) (Elsevier). * Associate Editor: [Living Journal of Computational Molecular Science](https://www.livecomsjournal.org/), LIveCoMS (Univ. of Colorado). * Editorial Board member: [International Journal of Quantum Chemistry](https://onlinelibrary.wiley.com/journal/1097461x) (Wiley); [Frontiers in Chemistry](https://www.frontiersin.org/journals/chemistry) (Frontiers); [Interdisciplinary Sciences: Computational Life Sciences](https://link.springer.com/journal/12539) (Springer) **Scientific Societies Memberships** * Société Chimique de France (SFC) * Royal Society of Chemistry (RSC) * American Chemical Society (ACS) * Biophysical Society * Association for Computing Machinery (ACM) * Sigma Xi
**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; Twitter: [@jppiquem](https://twitter.com/jppiquem) (personnel); [@piquemalgroup](https://twitter.com/PiquemalGroup) (équipe de recherche) Mastodon: [@piquemal@mastodon-pa.sorbonne-universite.fr](https://mastodon-pa.sorbonne-universite.fr/@piquemal) LinkedIn: [@jppiquem](https://www.linkedin.com/in/jppiquem/) **Recherche** * Chimie quantique; * Simulation moléculaire; * Sciences du médicament; * Informatique incluant High Performance Computing, Quantum Computing et Machine Learning. **Situation actuelle** * Professeur de classe exceptionnelle (PREX2) en Chimie Théorique, [Sorbonne Université](http://www.sorbonne-universite.fr/) (Paris, France); * Directeur du [Laboratoire de Chimie Théorique, UMR 7616 Sorbonne Université & CNRS, UFR de Chimie;](http://www.lct.jussieu.fr) * PI du projet [EMC2 (Extreme-scale Mathematically-based Computational Chemistry)](https://erc-emc2.eu/), ERC Synergy; * Research Adjunct Professor, [Department of Biomedical Engineering](https://www.bme.utexas.edu/), The University of Texas at Austin (USA); * Membre du comité scientifique de [PRACE](https://prace-ri.eu/) (Partnership for Advanced Computing in Europe). * Editeur, [Results in Chemistry](https://www.journals.elsevier.com/results-in-chemistry) (Elsevier). **Liste de publications mise à jour et Bibliométrie :** Visitez mon profil [Google scholar](https://scholar.google.com/citations?user=z0cOrb0AAAAJ&hl=fr) ou visitez ma page web : [http://piquemalresearch.com/publications/](http://piquemalresearch.com/publications/ "Jean-Philip Piquemal publications") **Développement logiciel** Développement du logiciel Tinker-HP: dynamique moléculaire ([https://tinker-hp.org](https://tinker-hp.org "Tinker-HP")). **Situation professionnelle** * 2023-présent : Professeur de classe exceptionnelle (PREX2), CNU section 31, SU. * 2020-présent : Membre du comité scientifique de [PRACE](https://prace-ri.eu/) (Partnership for Advanced Computing in Europe). * 2020-présent : Co-fondateur (2020) et directeur scientifique (CSO) de [Qubit Pharmaceuticals](https://www.qubit-pharmaceuticals.com/) * 2019-présent : Directeur du [Laboratoire de Chimie Théorique (LCT)](http://www.lct.jussieu.fr), UFR de Chimie, SU & CNRS * 2019-présent : chef d'équipe, Extreme-scale Mathematically-based Computational Chemistry (EMC2), [LCT](http://www.lct.jussieu.fr), SU/CNRS. * 2019-présent : PI du [projet ERC Synergy EMC2](https://erc-emc2.eu/) (2019-2025) * 2015-présent : Professeur adjoint de recherche, [Department of Biomedical Engineering](https://www.bme.utexas.edu/), The University of Texas at Austin (USA). * 2019-2023 : Professeur de classe exceptionnelle (PREX1), CNU section 31, SU. * 2016-2021 : Membre junior de l'[Institut Universitaire de France](https://www.iufrance.fr/) * 2016-2019 : Professeur (première classe, PR1), CNU section 31, SU. * 2012-2019 : chef d'équipe MC2, projet interdisciplinaire au sein de l'[ISCD](http://iscd.upmc.fr/) (Institute for Computations and data), SU. * 2012-2018 : Directeur de l'Institut Parisien de Chimie Physique et Théorique ([IP2CT](http://www.ip2ct.upmc.fr/)), 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](https://www.niehs.nih.gov), 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. \[[Academic Genealogy](https://academictree.org/chemistry/tree.php?pid=70959)\] * 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** * 2022: Prix: [HPC Innovation Excellence Award](https://www.hpcwire.com/off-the-wire/hyperion-research-announces-winners-of-hpc-innovation-excellence-awards/) . * 2022: H2020 Innovative Training Networks (ITN), Co-PI du projet [PHYMOL](http://www.phymol.eu/) (Marie Skłodowska–Curie Actions Doctoral Network sur les interactions intermoléculaires). * 2022: Fellow de la [Royal Society of Chemistry](https://www.rsc.org/) (FSRC, UK) * 2022: Nominé parmi les [100 meilleurs inventeurs francais de l'année](https://www.lepoint.fr/sciences-nature/les-meilleurs-inventeurs-francais-sont-09-06-2022-2478893_1924.php) par le journal Le Point * 2022: Prix d'innovation [i-Nov](https://www.enseignementsup-recherche.gouv.fr/fr/le-concours-i-nov-49817) (BPI France/MESRI) * 2021: Programme d'innovation [EIC-Accelerator](https://eic.ec.europa.eu/eic-funding-opportunities/eic-accelerator_en) (European Research Council) * 2020: Prix d'innovation [i-Lab](https://www.enseignementsup-recherche.gouv.fr/fr/le-concours-i-lab-49808) (BPI France/MESRI) * 2018: [ERC Synergy](https://erc.europa.eu/funding/synergy-grants), co-PI du projet Extreme-scale Mathematically-based Computational Chemistry (EMC2) avec E. Cancès, L. Grigori et Y. Maday * 2018: Prix [Atos Joseph Fourier](https://fr.wikipedia.org/wiki/Prix_Atos_-_Joseph_Fourier) en simulation numérique (1er prix) * 2018: Récipiendaire du [Fond France-Berkeley](https://fbf.berkeley.edu/) * 2016: Nominé en tant que membre junior de l'[Institut Universitaire de France](https://en.wikipedia.org/wiki/Institut_Universitaire_de_France) (chaire de recherche 2016-2021) * 2012: Récipiendaire du Fond Emergence-UPMC * 2011: Prix [Wiley-International Journal of Quantum Chemistry Young Investigator Award](https://sanibelsymposium.qtp.ufl.edu/awards-poster-sizes/winners/) * 2008: Récipiendaire du [Fond France-Canada pour la recherche](https://francecanadaculture.org/france-canada-research-fund/) * 2004: Bourse de recherche postdoctorale du National Institute of Health (NIH) - Visiting Fellowship (2004-2006) * 2001: Doctorat, financement du ministère de l'enseignement supérieur, de la recherche et de l'innovation (MESRI; 2001-2004) **Industrie** * Co-fondateur (2020) et directeur scientifique (CSO) de [Qubit Pharmaceuticals](https://qubit-pharmaceuticals.com/) **Activités Editoriales** * Editeur: [Results in Chemistry](https://www.journals.elsevier.com/results-in-chemistry) (Elsevier). * Editeur associé: [Living Journal of Computational Molecular Science](https://www.livecomsjournal.org/), LIveCoMS (Univ. of Colorado). * Membre de comités de lecture : [International Journal of Quantum Chemistry](https://onlinelibrary.wiley.com/journal/1097461x) (Wiley); [Frontiers in Chemistry](https://www.frontiersin.org/journals/chemistry) (Frontiers); [Interdisciplinary Sciences: Computational Life Sciences](https://link.springer.com/journal/12539) (Springer) **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

Publications

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
2023
Pré-publication, Document de travail hal-04172808v1

Advancing Force Fields Parameterization: A Directed Graph Attention Networks Approach

G. Chen , T. Jaffrelot Inizan , T. Plé , L. Lagardère , Jean-Philip Piquemal
2023
Pré-publication, Document de travail hal-04358188v1

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

Louis Lagardère , Lise Maurin , Olivier Adjoua , Krystel EL Hage , Pierre Monmarché
2023
Pré-publication, Document de travail hal-04162777v1

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

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

C. Feniou , B. Claudon , M. Hassan , A. Courtat , O. Adjoua
2023
Pré-publication, Document de travail hal-04146321v1

Leveraging Analog Quantum Computing with Neutral Atoms for Solvent Configuration Prediction in Drug Discovery

M. D’arcangelo , D. Loco , Team Fresnel , Nicolaï Gouraud , S. Angebault
2023
Pré-publication, Document de travail hal-04214318v1

β-actin plasticity is modulated by coordinated actions of histidine 73 methylation, nucleotide type, and ions

Adrien Schahl , Louis Lagardère , Brandon Walker , Pengyu Ren , Antoine Jégou
2022
Pré-publication, Document de travail hal-03904639v1

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

F. Célerse , L. Lagardère , Y. Bouchibti , F. Nachon , L. Verdier
ACS Catalysis, 2024, ⟨10.1021/acscatal.3c05560⟩
Article dans une revue hal-04290006v1

Sparse Quantum State Preparation for Strongly Correlated Systems.

C. Feniou , O. Adjoua , B. Claudon , J. Zylberman , E. Giner
Journal of Physical Chemistry Letters, 2024, 15 (11), pp.3197-3205. ⟨10.1021/acs.jpclett.3c03159⟩
Article dans une revue hal-04272837v1
Image document

Scalable Hybrid Deep Neural Networks/Polarizable Potentials Biomolecular Simulations including Long-range Effects

Théo Jaffrelot-Inizan , Thomas Plé , Olivier Adjoua , Pengyu Ren , Hatice Gökcan
Chemical Science, 2023, 14 (5438-5452), ⟨10.1039/D2SC04815A⟩
Article dans une revue hal-03738403v1

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

Pier Paolo Poier , Louis Lagardère , Jean-Philip Piquemal
Journal of Chemical Physics, 2023, 159 (15), pp.154109. ⟨10.1063/5.0166476⟩
Article dans une revue hal-04153125v1

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

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

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

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, pp.e1664. ⟨10.1002/wcms.1664⟩
Article dans une revue hal-03698549v1

QM / AMOEBA description of properties and dynamics of embedded molecules

Michele Nottoli , Mattia Bondanza , Patrizia Mazzeo , Lorenzo Cupellini , Carles Curutchet
WIREs Computational Molecular Science, 2023, ⟨10.1002/wcms.1674⟩
Article dans une revue hal-04122813v1

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

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

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
Journal of Chemical Theory and Computation, 2023, ⟨10.1021/acs.jctc.2c01233⟩
Article dans une revue hal-03887583v1

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

Overlap-ADAPT-VQE: Practical Quantum Chemistry on Quantum Computers via Overlap-Guided Compact Ansätze

César Feniou , Muhammad Hassan , Diata Traoré , Emmanuel Giner , Yvon Maday
Communications Physics, 2023, 6 (1), pp.192. ⟨10.1038/s42005-023-01312-y⟩
Article dans une revue hal-03955111v1
Image document

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
Journal of Chemical Theory and Computation, 2022, 18 (2), pp.968-977. ⟨10.1021/acs.jctc.1c01024⟩
Article dans une revue hal-03360596v1

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⟩
Article dans une revue hal-03706599v1

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
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
Image document

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

Pier Paolo Poier , Théo Jaffrelot Inizan , Olivier Adjoua , Louis Lagardère , Jean-Philip Piquemal
Journal of Physical Chemistry Letters, 2022, 13 (19), pp.4381-4388. ⟨10.1021/acs.jpclett.2c00936⟩
Article dans une revue hal-03624156v1

Computationally driven discovery of targeting SARS-CoV-2 Mpro inhibitors: from design to experimental validation

Léa El Khoury , Zhifeng Jing , Daniele Loco , Alberto Cuzzolin , Alessandro Deplano
Chemical Science, 2022, ⟨10.1039/D1SC05892D⟩
Article dans une revue hal-03361062v1

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

S. Naseem Kahn , L. Lagardère , C. Narth , G. A. Cisneros , P. Ren
Journal of Chemical Theory and Computation, 2022, 18 (6), pp.3607-3621. ⟨10.1021/acs.jctc.2c00029⟩
Article dans une revue hal-03508892v1

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⟩
Article dans une revue hal-03501135v1
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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⟩
Article dans une revue hal-03806627v1

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
Journal of Chemical Physics, 2021, ⟨10.1063/5.0072380⟩
Article dans une revue hal-03353343v1
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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
WIREs Computational Molecular Science, 2021, 11 (2), pp.e1497. ⟨10.1002/wcms.1497⟩
Article dans une revue hal-02921299v1

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

Frédéric Célerse , Louis Lagardère , Etienne Derat , Jean-Philip Piquemal
Journal of Chemical Theory and Computation, 2021, 17 (5), pp.3235-3236. ⟨10.1021/acs.jctc.1c00405⟩
Article dans une revue hal-03210774v1

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
Journal of Physical Chemistry Letters, 2021, 12, pp.6218-6226. ⟨10.1021/acs.jpclett.1c01460⟩
Article dans une revue hal-03220156v1
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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
Journal of Physical Chemistry Letters, 2021, 12 (34), pp.8285-829. ⟨10.1021/acs.jpclett.1c01722⟩
Article dans une revue hal-03132347v1

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⟩
Article dans une revue hal-03210111v1

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

Rae Corrigan , Guowei Qi , Andrew Thiel , Jack Lynn , Brandon D Walker
Journal of Chemical Theory and Computation, 2021, ⟨10.1021/acs.jctc.0c01286⟩
Article dans une revue hal-03183306v1
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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
Chemical Science, 2021, 12 (13), pp.4889-4907. ⟨10.1039/D1SC00145K⟩
Article dans une revue hal-02943694v1

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⟩
Article dans une revue hal-02912013v1
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Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems

Olivier Adjoua , Louis Lagardère , Luc-Henri Jolly , Arnaud Durocher , Thibaut Véry
Journal of Chemical Theory and Computation, 2021, 17 (4), pp.2034-2053. ⟨10.1021/acs.jctc.0c01164⟩
Article dans une revue hal-03179730v1

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

Rubén Laplaza , Francesca Peccati , Roberto A. Boto , Chaoyu Quan , Alessandra Carbone
WIREs Computational Molecular Science, 2021, 11 (2), ⟨10.1002/wcms.1497⟩
Article dans une revue hal-04028647v1
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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⟩
Article dans une revue hal-02504716v1

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

M. Devillers , Jean-Philip Piquemal , L. Salmon , N. Gresh
Journal of Computational Chemistry, 2020, 41 (8), pp.839-854. ⟨10.1002/jcc.26134⟩
Article dans une revue hal-02377726v1

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⟩
Article dans une revue hal-02410854v1
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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
Journal of Chemical Theory and Computation, 2020, 16 (4), pp.2013 - 2020. ⟨10.1021/acs.jctc.9b01204⟩
Article dans une revue hal-03046841v1
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A New Way for Probing Bond Strength

J. Klein , H. Khartabil , J.C. Boisson , J. Contreras-Garcia , Jean-Philip Piquemal
Journal of Physical Chemistry A, 2020, 124 (9), pp.1850-1860. ⟨10.1021/acs.jpca.9b09845⟩
Article dans une revue hal-02377737v1

NCIPLOT4: fast, robust and quantitative analysis of noncovalent interactions

Roberto A Boto , Francesca Peccati , Rubén Laplaza , Chaoyu Quan , Alessandra Carbone
Journal of Chemical Theory and Computation, 2020, ⟨10.1021/acs.jctc.0c00063⟩
Article dans une revue hal-02377999v1

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
Frontiers in Chemistry, 2020, 8, pp.440. ⟨10.3389/fchem.2020.00440⟩
Article dans une revue hal-02377718v1

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
Journal of Chemical Physics, 2020, 153, pp.024101. ⟨10.1063/5.0005060⟩
Article dans une revue hal-02314428v1

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⟩
Article dans une revue hal-02299827v1

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⟩
Article dans une revue hal-02122209v1
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How to make continuum solvation incredibly fast in a few simple steps: a practical guide to the domain decomposition paradigm for the Conductor-like Screening Model Continuum Solvation, Linear Scaling, Domain Decomposition

Benjamin Stamm , Louis Lagardère , Giovanni Scalmani , Paolo Gatto , Eric Cancès
International Journal of Quantum Chemistry, 2019, 119, pp.e25669. ⟨10.1002/qua.25669⟩
Article dans une revue hal-01793770v1
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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
PeerJ Physical Chemistry, 2019, 1, pp.e6. ⟨10.7717/peerj-pchem.6⟩
Article dans une revue hal-02372493v1
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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
Living Journal of Computational Molecular Science, 2019, 1 (2), ⟨10.33011/livecoms.1.2.10409⟩
Article dans une revue hal-02147771v2

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⟩
Article dans une revue hal-02142886v1

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
Chemical Science, 2019, ⟨10.1039/C9SC01745C⟩
Article dans une revue hal-02152908v1

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

Dmitry Bedrov , Jean-Philip Piquemal , Oleg V. Borodin , Alexander Mackerell , Benoît Roux
Chemical Reviews, 2019, ⟨10.1021/acs.chemrev.8b00763⟩
Article dans une revue hal-02144165v1
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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⟩
Article dans une revue hal-02283625v1
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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
Annual Reviews of Biophysics, 2019, 48, pp.371-394. ⟨10.1146/annurev-biophys-070317-033349⟩
Article dans une revue hal-01821899v1

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids

Changsheng Zhang , Chao Lu , Zhifeng F Jing , Chuanjie Wu , Jean-Philip Piquemal
Journal of Chemical Theory and Computation, 2018, 14 (4), pp.2084-2108. ⟨10.1021/acs.jctc.7b01169⟩
Article dans une revue hal-02126772v1

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⟩
Article dans une revue hal-02126731v1

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⟩
Article dans une revue hal-02126841v1

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
Journal of Physical Chemistry B, 2018, 122 (24), pp.6371-6376. ⟨10.1021/acs.jpcb.8b03194⟩
Article dans une revue hal-02126853v1
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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
Chemical Science, 2018, 9, pp.956-972 ⟨10.1039/C7SC04531J⟩
Article dans une revue hal-01648245v3
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Tinker 8: Software Tools for Molecular Design

Joshua A Rackers , Zhi Wang , Chao Lu , Marie L Laury , Louis Lagardere
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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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
ChemPhysChem, 2018, 19 (6), pp.724-735. ⟨10.1002/cphc.201701325⟩
Article dans une revue hal-03377532v1
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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
Journal of Chemical Physics, 2018, 149 (12), pp.124103. ⟨10.1063/1.5044541⟩
Article dans une revue hal-01897263v1

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
Journal of Physical Chemistry B, 2017, 121 (26), pp.6295-6312. ⟨10.1021/acs.jpcb.7b01053⟩
Article dans une revue hal-02126854v1
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The Truncated Conjugate Gradient (TCG), a Non-iterative/Fixed-cost Strategy for Computing Polarization in Molecular Dynamics: Fast Evaluation of Analytical Forces

Félix Aviat , Louis Lagardère , Jean-Philip Piquemal
Journal of Chemical Physics, 2017, 147 (16), pp.161724. ⟨10.1063/1.4985911⟩
Article dans une revue hal-01571663v2
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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
Journal of Computational Chemistry, 2017, 121, pp.3997 - 1920. ⟨10.1021/acs.jpcb.7b01836⟩
Article dans une revue hal-01571959v1
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Channeling Through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li + , Na + , K + and Rb + Series. Assessment of the Accuracy of the SIBFA Anisotropic Polarizable Molecular Mechanics Potential

Nohad Gresh , Sehr Naseem-Khan , Louis Lagardère , Jean-Philip Piquemal , Judit E. Sponer
Journal of Physical Chemistry B, 2017, ⟨10.1021/acs.jpcb.7b01836⟩
Article dans une revue hal-01502376v1
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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
Biochemical and Biophysical Research Communications, 2017, ⟨10.1016/j.bbrc.2017.05.001⟩
Article dans une revue hal-01520237v1

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⟩
Article dans une revue hal-02126842v1

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

Joshua A. Rackers , Qiantao Wang , Chengwen Liu , Jean-Philip Piquemal , Pengyu Ren
Physical Chemistry Chemical Physics, 2017, ⟨10.1039/C6CP06017J⟩
Article dans une revue hal-01405847v1
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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
Journal of Computational Chemistry, 2017, 38 (23), pp.2047-2055. ⟨10.1002/jcc.24853⟩
Article dans une revue hal-01571313v1
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Towards scalable and accurate molecular dynamics using the SIBFA polarizable force field

Louis Lagardère , Léa El-Khoury , Sehr Naseem-Khan , Félix Aviat , Nohad Gresh
AIP Conference Proceedings, 2017
Article dans une revue hal-01521838v1
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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
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
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
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
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⟩
Article dans une revue hal-01171804v1
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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
Journal of Chemical Theory and Computation, 2016, 12 (8), pp.3654-3661. ⟨10.1021/acs.jctc.6b00385⟩
Article dans une revue hal-02126716v1
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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
Journal of Computational Chemistry, 2016, 37 (5), pp.494-506. ⟨10.1002/jcc.24257⟩
Article dans une revue hal-01223008v1

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

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
Journal of Computational Chemistry, 2016, 37 (32), pp.2770-2782. ⟨10.1002/jcc.24503⟩
Article dans une revue hal-02126855v1

Polarizable Molecular Dynamics in a Polarizable Continuum Solvent

Filippo Lipparini , Louis Lagardère , Christophe Raynaud , Benjamin Stamm , Eric Cancès
Journal of Chemical Theory and Computation, 2015, 11 (2), pp.623-634. ⟨10.1021/ct500998q⟩
Article dans une revue hal-01114784v1

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
Journal of Computational Chemistry, 2015, 36 (5), pp.285-302. ⟨10.1002/jcc.23801⟩
Article dans une revue hal-02126857v1

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⟩
Article dans une revue hal-02126858v1

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⟩
Article dans une revue hal-01397958v1
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Entasis Through Hook-and-Loop Fastening in a Glycoligand with Cumulative Weak Forces Stabilizing Cu(I).

Ludivine Garcia , Federico Cisnetti , Natacha Gillet , Régis Guillot , Magali Aumont-Nicaise
Journal of the American Chemical Society, 2015, 137 (3), pp.1141-1146. ⟨10.1021/ja510259p⟩
Article dans une revue hal-01101575v1

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
Journal of Chemical Theory and Computation, 2015, 11 (6), pp.2589-2599. ⟨10.1021/acs.jctc.5b00171⟩
Article dans une revue hal-01223161v1

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⟩
Article dans une revue hal-02126856v1
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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
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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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

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
Journal of Physical Chemistry B, 2015, 119 (30), pp. 9477-9495. ⟨10.1021/acs.jpcb.5b01695⟩
Article dans une revue hal-01287484v1

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
Physical Chemistry Chemical Physics, 2014, 16, pp.9876-9891. ⟨10.1039/C3CP52774C⟩
Article dans une revue hal-01131254v1

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
Journal of Molecular Modeling, 2014, 20 (11), ⟨10.1007/s00894-014-2472-5⟩
Article dans une revue hal-02126794v1

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⟩
Article dans une revue hal-02126859v1

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
Journal of Chemical Physics, 2014, 141 (18), pp.184108. ⟨10.1063/1.4901304⟩
Article dans une revue hal-01090954v1

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⟩
Article dans une revue hal-02126797v1

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
Journal of Chemical Theory and Computation, 2014, 10 (5), pp.1900-1909. ⟨10.1021/ct4006135⟩
Article dans une revue hal-02126798v1

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
Journal of Computational Chemistry, 2014, 35 (29), pp.2096-2106. ⟨10.1002/jcc.23724⟩
Article dans une revue hal-01081843v1

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⟩
Article dans une revue hal-02126862v1

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
Journal of Physical Chemistry Letters, 2014, 5, pp.953-958. ⟨10.1021/jz5002506⟩
Article dans une revue hal-00956401v1
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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
Article dans une revue hal-00960389v1
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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⟩
Article dans une revue hal-01146475v1

Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations

Filippo Lipparini , Louis Lagardère , Benjamin Stamm , Eric Cancès , Michael Schnieders
Journal of Chemical Theory and Computation, 2014, 10 (4), pp.1638-1651. ⟨10.1021/ct401096t⟩
Article dans une revue hal-01090942v1

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
Journal of Molecular Modeling, 2014, 20, pp.2471. ⟨10.1007/s00894-014-2471-6⟩
Article dans une revue hal-01157657v1

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⟩
Article dans une revue hal-01287209v1

Synthesis and structure–activity relationship of non-peptidic antagonists of neuropilin-1 receptor

Wang-Qing Liu , Valentino Megale , Lucia Borriello , Bertrand Leforban , Matthieu Montes
Bioorganic and Medicinal Chemistry Letters, 2014, 24 (17), pp.4254-4259. ⟨10.1016/j.bmcl.2014.07.028⟩
Article dans une revue hal-02126861v1

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
Journal of Physical Chemistry B, 2014, 118 (24), pp.6456-6465. ⟨10.1021/jp411671a⟩
Article dans une revue hal-02126799v1

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
Journal of Physical Chemistry A, 2014, 118 (35), pp.7598-7612. ⟨10.1021/jp5051657⟩
Article dans une revue hal-01287208v1

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⟩
Article dans une revue hal-00926680v1

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⟩
Article dans une revue hal-00880177v1

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⟩
Article dans une revue hal-02126863v1

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⟩
Article dans une revue hal-02126864v1
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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⟩
Article dans une revue hal-00875425v1

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⟩
Article dans une revue hal-02126839v1

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⟩
Article dans une revue hal-02126800v1

Coupling Quantum Interpretative Techniques: Another Look at Chemical Mechanisms in Organic Reactions

Natacha Gillet , Robin Chaudret , Julia Contreras-García , Weitao Yang , Bernard Silvi
Journal of Chemical Theory and Computation, 2012, 8 (11), pp.3993-3997. ⟨10.1021/ct300234g⟩
Article dans une revue hal-02126838v1

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⟩
Article dans une revue hal-02126868v1

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⟩
Article dans une revue hal-02126866v1

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⟩
Article dans une revue hal-02126837v1

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
Theoretical Chemistry Accounts: Theory, Computation, and Modeling, 2012, 131 (March), pp.1198. ⟨10.1007/s00214-012-1198-7⟩
Article dans une revue hal-00904389v1

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⟩
Article dans une revue hal-02127244v1

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
Proteins - Structure, Function and Bioinformatics, 2011, 79 (1), pp.203-220. ⟨10.1002/prot.22873⟩
Article dans une revue hal-02126875v1
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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
Journal of Computational Chemistry, 2011, 32 (6), pp.1178-1182. ⟨10.1002/jcc.21698⟩
Article dans une revue hal-00992047v1

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⟩
Article dans une revue hal-02126872v1

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⟩
Article dans une revue hal-02126873v1

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⟩
Article dans une revue hal-02126869v1

Interactions within the alcohol dehydrogenase Zn(II)-metalloenzyme active site: Interplay between subvalence, electron correlation/dispersion, and charge transfer/induction effects

Benoit de Courcy , Jean-Pierre Dognon , Carine Clavaguéra , Nohad Gresh , Jean-Philip Piquemal
International Journal of Quantum Chemistry, 2011, 111 (6), pp.1213-1221. ⟨10.1002/qua.22760⟩
Article dans une revue hal-00926669v1
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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⟩
Article dans une revue hal-00874618v1

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⟩
Article dans une revue hal-02126836v1

NCIPLOT: A Program for Plotting Noncovalent Interaction Regions

Julia Contreras-García , Erin Johnson , Shahar Keinan , Robin Chaudret , Jean-Philip Piquemal
Journal of Chemical Theory and Computation, 2011, 7 (3), pp.625-632. ⟨10.1021/ct100641a⟩
Article dans une revue hal-02126834v1

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
Catalysis Today, 2011, 177 (1), pp.79-86. ⟨10.1016/j.cattod.2011.07.015⟩
Article dans une revue hal-02126870v1

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
Journal of Physical Chemistry B, 2011, 115 (25), pp.8304-8316. ⟨10.1021/jp2024654⟩
Article dans une revue hal-02126871v1

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
Journal of Chemical Theory and Computation, 2010, 6 (4), pp.1048-1063. ⟨10.1021/ct100089s⟩
Article dans une revue hal-00996393v1

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
Journal of Physical Chemistry B, 2010, 114 (14), pp.4884-4895. ⟨10.1021/jp907629k⟩
Article dans une revue hal-00494595v1

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⟩
Article dans une revue hal-02127241v1

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⟩
Article dans une revue hal-02126831v1

Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field

Johnny Wu , Jean-Philip Piquemal , Robin Chaudret , Peter Reinhardt , Pengyu Ren
Journal of Chemical Theory and Computation, 2010, 6 (7), pp.2059-2070. ⟨10.1021/ct100091j⟩
Article dans une revue hal-02126833v1

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
Journal of the American Chemical Society, 2010, 132 (34), pp.11860-3. ⟨10.1021/ja103996q⟩
Article dans une revue hal-00915204v1

Role of Cation Polarization in holo- and hemi- Directed [Pb(H 2 O) n ] 2+ Complexes and Development of a Pb 2+ Polarizable Force Field

Mike Devereux , Marie-Céline van Severen , Olivier Parisel , Jean-Philip Piquemal , Nohad Gresh
Journal of Chemical Theory and Computation, 2010, 7 (1), pp.138-147. ⟨10.1021/ct1004005⟩
Article dans une revue hal-02126874v1

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⟩
Article dans une revue hal-02126877v1

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

C. Gourlaouen , O. Parisel , J.-P. Piquemal
Journal of Chemical Physics, 2010, 133 (12), pp.124310. ⟨10.1063/1.3491266⟩
Article dans une revue hal-02126876v1

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
Article dans une revue hal-00494585v1

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⟩
Article dans une revue hal-02126822v1

Progress Towards Accurate Molecular Modeling of Metal Complexes Using Polarizable Force Fields

R. Chaudret , S. Ulmer , M.-C. van Severen , N. Gresh , O. Parisel
AIP Conference Proceedings, 2009, 1102, pp.185-192. ⟨10.1063/1.3108373⟩
Article dans une revue hal-02126821v1

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⟩
Article dans une revue hal-02126826v1

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⟩
Article dans une revue hal-02126824v1

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⟩
Article dans une revue hal-02126828v1

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
Inorganic Chemistry, 2009, 48 (15), pp.7003-7005. ⟨10.1021/ic900567z⟩
Article dans une revue hal-02126825v1

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⟩
Article dans une revue hal-02126830v1

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⟩
Article dans une revue hal-02126823v1

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
International Journal of Quantum Chemistry, 2008, 108 (11), pp.1951-1969. ⟨10.1002/qua.21711⟩
Article dans une revue hal-02126817v1

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⟩
Article dans une revue hal-02126878v1

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⟩
Article dans une revue hal-02126818v1

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⟩
Article dans une revue hal-02126879v1

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
International Journal of Quantum Chemistry, 2008, 108 (11), pp.1905-1912. ⟨10.1002/qua.21675⟩
Article dans une revue hal-02126814v1

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⟩
Article dans une revue hal-02126819v1

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⟩
Article dans une revue hal-02126810v1

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⟩
Article dans une revue hal-02126881v1

Anisotropic, polarizable molecular mechanics studies of inter-, intramolecular interactions, and ligand-macromolecule complexes.A bottom-up strategy

Nohad Gresh , G. Andres Cisneros , T.A. Darden , J.-P. Piquemal
Journal of Chemical Theory and Computation, 2007, 3, pp.1960
Article dans une revue hal-00494588v1

Binding of 5-Phospho-D-Arabinonohydoxamate and 5-Phospho-D-Arabinonate Inhibitors to Zinc Phosphomannoisomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics.

Nohad Gresh , Clément Roux , N. Gresh , L. E. Perera , J.-P. Piquemal
Journal of Computational Chemistry, 2007, 28, pp.938
Article dans une revue hal-00494629v1

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 hal-02126880v1

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

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
Journal of the American Chemical Society, 2007, 131, pp.11067
Article dans une revue hal-00494580v1

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 hal-02127159v1

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
Journal of Chemical Physics, 2006, 125 (18), pp.184101. ⟨10.1063/1.2363374⟩
Article dans une revue hal-02126808v1

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
Journal of Chemical Physics, 2006, 125 (5), pp.054511. ⟨10.1063/1.2234774⟩
Article dans une revue hal-02126806v1

Towards a force field based on density fitting

Nohad Gresh , J.-P. Piquemal , G. Andres Cisneros , P. Reinhardt , T.A. Darden
Journal of Chemical Physics, 2006, 124, pp.104101
Article dans une revue hal-00494627v1

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

[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
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

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

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

Intermolecular electrostatic energies using density fitting

G. Andrés Cisneros , Jean-Philip Piquemal , Thomas Darden
Journal of Chemical Physics, 2005, 123 (4), pp.044109. ⟨10.1063/1.1947192⟩
Article dans une revue hal-02126804v1

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
Journal of Computational Chemistry, 2003, 24 (16), pp.1963-1970. ⟨10.1002/jcc.10354⟩
Article dans une revue hal-02127138v1

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

VTX: High-performance molecular structure and dynamics visualization software

Maxime Maria , Simon Guionnière , Nicolas Dacquay , Yassine Naïmi , Jean-Philip Piquemal
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
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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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
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
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
Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications, Springer Netherlands, pp.137-172, 2009
Chapitre d'ouvrage hal-02127328v1