CV of Jean-Philip Piquemal

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〉

Zhifeng Jing, Chengwen Liu, Sara Cheng, Rui Qi, Brandon Walker, et al.. Polarizable force fields for biomolecular simulations: Recent advances and applications. annual review of biophysics, 2018. 〈hal-01821899〉

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, In press, 〈10.1002/qua.25669〉. 〈hal-01793770〉

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. 〈hal-01820747〉

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〉

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. 〈http://aip.scitation.org/doi/10.1063/1.4985911〉. 〈10.1063/1.4985911〉. 〈hal-01571663v2〉

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〉

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〉

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, 〈http://aip.scitation.org/journal/apc〉. 〈hal-01521838〉

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〉

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〉

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〉

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〉

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〉

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〉

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 Cances, 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. 〈http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00171〉. 〈10.1021/acs.jctc.5b00171〉. 〈hal-01223161〉

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〉

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〉

R. Chaudret, B. De Courcy, J. Contreras-García, E. 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〉

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 (ACS), 2014, 5, pp.953-958. 〈10.1021/jz5002506〉. 〈hal-00956401〉

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〉

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〉

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〉

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〉

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. 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〉

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〉

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〉

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〉

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.1178-82. 〈10.1002/jcc.21698〉. 〈hal-00992047〉

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〉

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〉

E. Gloaguen, B. De Courcy, J.-P. Piquemal, J. Pilme, 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.11860-11863. 〈10.1021/ja103996q〉. 〈hal-00520142〉

E. 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〉

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〉

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〉

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. J. Chem. Theory Comput., 2007, pp.1960. 〈hal-00494588〉

Nohad Gresh, C. 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, 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, 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〉. 〈http://www.panstanford.com/〉. 〈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〉. 〈http://www.springer.com/series/6918〉. 〈hal-01224203〉

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〉. 〈http://onlinelibrary.wiley.com/bookseries/10.1002/SERIES6143〉. 〈hal-01114184〉

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〉