Publications
Bibliometric Indicators
H-index: 59 (59 publications cited >= 59 times: source Google Scholar) (updated: 12/2024)
I10-index:151 (151 publications cited >= 10 times, source Google Scholar)
Total number of publications: 203 including Chemical Review (1), Nature Communications (1), Accounts of Chemical Research (1), WIREs Comp. Mol. Sci. (3), Ann. Rev. Biophys (1), ACS Cat. (1), J. Am. Chem. Soc. (4), Chem. Sci. (7), Commun Phys/Chem/Bio (3), J. Phys. Chem. Lett. (10), J. Chem. Theory. Comput. (40), JCIM(1), Chem. Com.(1), Front. Mol. Biosci (1), Chem. Euro. J. (2), Front. Chem (1), ChemPhysChem(2), Physical Review Research (1), J. Chem. Phys. (15), J. Comput. Chem. (20), J. Phys. Chem. A/B/C (19), Phys. Chem. Chem. Phys. (3), Physical Review A (1), Int. J. Quant. Chem. (4), Chem. Phys. Lett. (6)…
Updated Citation Metrics/publication list through direct link to Google Scholar
ORCID: 0000-0001-6615-9426
Note: DOI hyperlinks allow to reach the papers’s publisher version. If you do not have a subscription access, ALL my papers are in Free Access either through direct publisher [Open Access], [HAL], NIH Pubmed Central [PMC Free Text] servors or via preprint servors ([ChemRxiv], [Arxiv]…). PDFs are for internal use.
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- Theoretical study of phenol and 2-Aminophenol docking at a model of tyrosinase active site.
J-P. Piquemal, J. Maddaluno, B. Silvi, C. Giessner-Prettre, New J. Chem., 2003, 27, 909-913.[PDF][HAL]
DOI: 10.1039/B210307A - Improved formulas for the calculation of the electrostatic contribution to intermolecular interaction energy from multipolar expansion of the electronic distribution.
J-P. Piquemal, N. Gresh, C. Giessner-Prettre, J. Phys. Chem. A, 2003, 107, 10353.[PDF][HAL]
DOI: 10.1021/jp035748t - Inclusion of the ligand field contribution in a polarizable molecular mechanics : SIBFA LF.
J-P. Piquemal, B. Williams-Hubbard, N. Fey, R.J. Deeth, N.Gresh, C. Giessner-Prettre, J. Comput. Chem., 2003, 24, 1963 [PDF][HAL]
DOI: 10.1002/jcc.10354 - A CSOV Study of the difference between HF and DFT Intermolecular Interaction Energy Values : the importance of the charge transfer contribution.
J-P. Piquemal, A. Marquez, O. Parisel, C. Giessner-Prettre, J. Comput. Chem. 2005, 26, 1052 [PDF][HAL]
DOI: 10.1002/jcc.20242 - Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-b-lactamase by polarizable molecular mechanics. Validation on model binding sites with parallel quantum-chemistry computations.
J. Antony, J-P. Piquemal, N. Gresh, J. Comput. Chem., 2005, 26, 1131 [PDF][HAL]
DOI: 10.1002/jcc.20245 - Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contribution of the intermolecular interaction energy. Comparisons with parallel ab initio computations.
N. Gresh, J-P. Piquemal, M. Krauss, J. Comput. Chem., 2005, 26, 1113 [PDF][HAL]
DOI: 10.1002/jcc.20244 - Intermolecular Electrostatic Energies using Density Fitting.
G. A. Cisneros, J-P. Piquemal, T. A. Darden, J. Chem. Phys., 2005, 123, 044109 [PDF] [HAL]PMC Free Text]
DOI: 10.1063/1.1947192 - Revisiting the geometry of nd10 (n+1)s0 [M(H2O)]p+ complexes using 4-component relativistic DFT calculations and scalar relativistic correlated CSOV energy decompositions (Mn+ = Cu+, Zn2+, Ag+, Cd2+, Au+, Hg2+).
C. Gourlaouen, J-P. Piquemal, T. Saue, O. Parisel, J. Comput. Chem., 2006, 27, 2, 142 [PDF][HAL]
DOI: 10.1002/jcc.20329 - Towards a Force Field based on Density Fitting.
J-P. Piquemal, G. A. Cisneros, P. Reinhardt, N. Gresh, T. A. Darden,
J. Chem. Phys., 2006, 124, 104101 [PDF] [HAL][PMC Free Text]
DOI: 10.1063/1.2173256 - Comments on the nature of the bonding in oxygenated dinuclear copper enzymes models.
J-P. Piquemal, J. Pilmé, J. Mol. Struct.: THEOCHEM, 2006, 764, 77 [PDF] [HAL][PMC Free Text]
DOI: 10.1016/j.theochem.2006.02.013 - Pb(H2O)]2+ and [Pb(OH)]+: four-component DFT calculations, correlated scalar relativistic CSOV energy decompositions, and topological analysis.
C. Gourlaouen, J-P. Piquemal, O. Parisel, J. Chem. Phys., 2006, 124, 17, 174311 [PDF][HAL]
DOI: 10.1063/1.2186994 - QM/MM Electrostatic Embedding with Continuous and Discrete Functions.
G. A. Cisneros, J-P. Piquemal, T. A. Darden, J. Phys. Chem. B. , 2006, 110, 13682 [PDF] [HAL][PMC Free Text]
DOI: 10.1021/jp062768x - Towards accurate solvation dynamics of divalent cations in water using the polarizable Amoeba force field: from energetics to structure.
J-P. Piquemal, L. Perera, G. A. Cisneros, P. Ren, L. G. Pedersen, T. A. Darden, J. Chem. Phys., 2006, 125, 054511 [PDF][HAL]
DOI: 10.1063/1.2234774 - Generalization of the Gaussian Electrostatic Model: extension to arbitrary angular momentum, distributed multipoles and speedup with reciprocal space methods.
G. A. Cisneros, J-P. Piquemal, T. A. Darden, J. Chem. Phys., 2006, 125, 184101 [PDF] [HAL][PMC Free Text]
DOI: 10.1063/1.2363374 - Binding of 5-Phospho-D-Arabinonohydroxamate and 5-Phospho-D-Arabinonate Inhibitors to Zinc Phosphomannose Isomerase from Candida albicans studied by polarizable Molecular Mechanics and Quantum mechanics.
C. Roux, N. Gresh, L. Perera, J-P Piquemal, L. Salmon, J. Comput. Chem., 2007, 28, 938 [PDF][HAL]
DOI: 10.1002/jcc.20586 - Towards a separate reproduction of the contributions to the Hartree-Fock and DFT intermolecular interaction energies by polarizable molecular mechanics with the SIBFA potential.
J-P Piquemal, H. Chevreau, N. Gresh, J. Chem. Theory. Comput., 2007, 3, 824 [PDF][HAL]
DOI: 10.1021/ct7000182 - Key role of the polarization anisotropy of water in modeling classical polarizable force fields.
J-P Piquemal, R. Chelli, P. Procacci, N. Gresh, J. Phys. Chem. A, 2007, 111, 8170 [PDF][HAL]
DOI: 10.1021/jp072687g - The Specificity of Acyl Transfer from 2-Mercaptobenzamide Thioesters to the HIV-1 Nucleocapsid Protein.
L. M. M. Jenkins, T. Hara, S. R. Durell, R. Hayashi, J. K. Inman, J-P Piquemal, N. Gresh, E. Appella, J. Am. Chem. Soc., 2007, 129, 11067 [PDF][HAL]
DOI: 10.1021/ja071254o - Anisotropic, polarizable molecular mechanics studies of inter-, intra-molecular interactions, and ligand-macromolecule complexes. A bottom-up strategy.
N. Gresh, G. A. Cisneros, T. A. Darden, J-P Piquemal, J. Chem. Theory. Comput., 2007, 3, 1960-1986. [PDF] [HAL][PMC Free Text]
DOI: 10.1021/ct700134r - Numerical fitting of molecular properties to Hermite Gaussians.
G. A. Cisneros, D. Elking, J-P Piquemal, T. A. Darden, J. Phys. Chem. A, 2007, 111, 12049.[PDF] [HAL][PMC Free Text]
DOI: 10.1021/jp074817r - Understanding lead chemistry from topological insights:the transition between holo- and hemidirected structures within the [Pb(CO)n]2+ model series.
C. Gourlaouen, H. Gérard, J.-P. Piquemal, O. Parisel, 2008, Chem. Eur. J., 14, 2730 [PDF][HAL]
DOI: 10.1002/chem.200701265 - Advancing beyond Charge Analysis using the Electronic Localization Function: Chemically Intuitive Distribution of Electrostatic Moments.
J. Pilmé, J-P Piquemal, 2008, J. Comput. Chem., 29, 1440. [PDF][HAL]
DOI: 10.1002/jcc.20904 - Simple formulas for improved point-charge electrostatics in classical force fields and hybrid Quantum Mechanical/Molecular Mechanical embedding.
G. A. Cisneros, S. Na-Im Tholander, D. Elking, T. A. Darden, O. Parisel, J-P Piquemal, Int. J. Quant. Chem., 2008, 108, 1905.[PDF] [HAL][PMC Free Text]
DOI: 10.1002/qua.21675 - What can be learnt on biological or biomimetic systems with the topological analysis of the electron localization function?
J-P Piquemal, J. Pilmé, O. Parisel, H. Gérard, I. Fourré, J. Bergès, C. Gourlaouen, A. de la Lande, M. C. van Severen, B. Silvi, Int. J. Quant. Chem., 2008, 108, 1951.[PDF][HAL]
DOI: 10.1002/qua.21711 - Energy analysis of Zn polycoordination in a metalloprotein environment and of the role of a neighboring aromatic residue. What is the impact of polarization?
B. de Courcy, J-P Piquemal, N. Gresh, J. Chem. Theo. Comput., 2008, 4, 1659 .[PDF][HAL]
DOI: 10.1021/ct800200j - Fragment-localized Kohn-Sham orbitals via a Singles-CI procedure and application to local properties and intermolecular energy decomposition analysis
P. Reinhardt, J-P Piquemal, A. Savin, J. Chem. Theo. Comput., 2008, 4, 2020 [PDF][HAL]
DOI: 10.1021/ct800242n - Design of next generation polarizable force fields from ab initio computations: beyond point charges.
G. A. Cisneros, T. A. Darden, N. Gresh, P. Reinhardt, O. Parisel, J. Pilmé, J-P Piquemal in Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications, for the Book Series: Challenges and Advances in Computational Chemistry and Physics , ed. D. M. York and T.-S. Lee, 2009, 137-172, Springer Verlag. Invited Book Chapter [HAL]
DOI:10.1007/978-1-4020-9956-4_6 - Progress towards accurate molecular modeling of metal complexes using polarizable force fields.
R. Chaudret, S. Ulmer, M-C van Severen, N. Gresh, O. Parisel, G. A. Cisneros , T. A. Darden, J-P Piquemal, AIP Conf. Proc., 2009, 1102, 185.[PDF][HAL]
DOI:10.1063/1.3108373 - Trends in ns2 np0 [M(CO)]p+ complexes: from germanium to element 114 (Uuq).
C. Gourlaouen, O. Parisel, J-P Piquemal, Chem. Phys. Lett. 2009, 469, 38-42 [PDF][HAL]
DOI: 10.1016/j.cplett.2008.12.040 - Importance of lone pair interactions/redistribution in hard and soft ligands within the active site of alcohol dehydrogenase Znmetalloenzyme: Insights from Electron Localization Function.
B. de Courcy, N. Gresh, J-P Piquemal, Interdiscip. Sci. Comput. Life Sci., 2009, 1, 55 [PDF][HAL]
DOI: 10.1007/s12539-008-0027-0 - New intermolecular benchmark calculations on the water dimer: SAPT and supermolecular post-Hartree-Fock approaches.
P. Reinhardt, J-P Piquemal, Int. J. Quant. Chem., 2009, 109, 3259. [PDF][HAL]
DOI: 10.1002/qua.22299 - Dioxygen Activation by Mononuclear Copper Enzymes: Insights From a Tripodal Ligand Mimicking their CuM Coordination Sphere.
A. de la Lande, D. Salahub, V. Moliner, H. Gérard, J-P Piquemal, O. Parisel, 2009, Inorg. Chem.(Communication), 4, 7003. [PDF][HAL]
DOI:10.1021/ic900567z - Beyond holo/hemidirectionality in Pb(II) complexes: can the valence lone pair be bisdirected?
M-C. van Severen, J.-P. Piquemal, O. Parisel, Chem. Phys. Lett., 2009, 478, 17 [PDF][HAL]
DOI: 10.1016/j.cplett.2009.07.036 - Synthesis and evaluation of non-hydrolyzable D-mannose 6- phosphate surrogates reveal 6-deoxy-6-dicarboxymethyl-Dmannose as a new strong inhibitor of phosphomannose isomerases.
J. Foret, B. de Courcy, N. Gresh, J-P. Piquemal, L. Salmon , Bioorg. Med. Chem., 2009, 17, 7100. [PDF][HAL]
DOI: 10.1016/j.bmc.2009.09.005 - The Gaussian Multipole Model.
D. Elking, G. A. Cisneros, J-P Piquemal, T. A. Darden and L. G. Pedersen, J. Chem. Theo. Comput., 2010, 6, 190 [PDF] [HAL][PMC Free Text]
DOI: 10.1021/ct900348b - Theoretical Study of the Docking of Competitive Inhibitors at a Model of Tyrosinase enzyme Active Site: joint broken symmetry/spin-flip DFT study.
A. de la Lande, J. Maddaluno, O. Parisel, T. A. Darden, J-P Piquemal, Interdiscip. Sci. Comput. Life Sci., 2010, 2, 3 [PDF] [HAL][PMC Free Text]
DOI: 10.1007/s12539-010-0096-8 - 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, J. Am. Chem. Soc., 2010, 132, 3312. [PDF][HAL]
DOI: 10.1021/ja9059156 - Lead substitution in synaptotagmin: a case study.
M-C. van Severen, J-P Piquemal, O. Parisel, J. Phys. Chem. B, 2010, 114, 4005 [PDF][HAL]
DOI:10.1021/jp910131r - 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.
N. Gresh, N. Audiffren, J-P. Piquemal, J. de Ruyck, M. Ledecq, J. Wouters, J. Phys. Chem. B, 2010, 114, 4884 [PDF] [HAL]
DOI:10.1021/jp907629k - 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, J. Pilmé, J-P Piquemal, J. Chem. Theory. Comput., 2010, 6, 1048 [PDF][HAL][PMC Free Text]
DOI: 10.1021/ct100089s - Editorial: Quantum Mechanical Modeling of Biological Systems.
J-P Piquemal and Dennis Salahub, Interdiscip. Sci. Comput. Life Sci., 2010, 2, 1 [PDF][HAL]
DOI: 10.1007/s12539-010-0001-5 - Polarizable molecular dynamics simulation of Zn(II) in water using the polarizable AMOEBA force field.
J. Wu., J.-P. Piquemal, R. Chaudret, P. Reinhardt, P. Ren, J. Chem. Theo. Comput., 2010, 6, 2059.[PMC Free Text][HAL][PDF]
DOI: 10.1021/ct100091j - Gas phase folding of a two-residue model peptide chain: on the importance of an interplay between experiment and theory.
E. Gloaguen, B. de Courcy, J-P Piquemal, J. Pilmé, O. Parisel, R. Pollet, H. S. Biswal, F. Piuzzi, B. Tardivel, M. Broquier, M. Mons, J. Am. Chem. Soc.(Communication), 2010, 132, 11860-11863. [PDF][HAL]
DOI: 10.1021/ja103996q - Importance of backdonation in [M(CO)]p+ complexes isoelectronic to [Au(CO)]+.
C. Gourlaouen, O. Parisel, J.-P. Piquemal, J. Chem. Phys., 2010, 133, 124310.[PDF][HAL]
DOI: 10.1063/1.3491266 - The reaction mechanism of type I phosphomannose isomerases: new informations from polarizable molecular mechanics and inhibition studies.
C. Roux, F. Bhatt, J. Forest, B. de Courcy, N. Gresh, J-P. Piquemal, C. J. Jeffery, L. Salmon, Proteins: Struct. Func. Bio., 2011, 79, 203-220 [PDF][HAL]
DOI: 10.1002/prot.22873 - The Role of Cation Polarization in holo- and hemi-Directed [Pb(H2O)n]2+ Complexes and Development of a Pb2+ Polarizable Force Field.
M. Devereux, M.-C. van Severen, O. Parisel, J-P Piquemal, N. Gresh, J. Chem. Theo. Comput., 2011, 7, 138-147.[PDF][HAL]
DOI: 10.1021/ct1004005 - Interactions within the Alcohol Dehydrogenase (ADH) Zn(II)-metalloenzyme active site: interplay between subvalence, electron correlation/dispersion and charge transfer/induction effects
B. de Courcy, J-P. Dognon, C. Clavaguera, N. Gresh, J-P. Piquemal, Int. J. Quant. Chem., 2011, 111, 1213. [PDF][HAL]
DOI: 10.1002/qua.22760 - Editorial: From Quantum Mechanics to Force Fields: new methodologies for the classical simulation of complex systems.
J.-P. Piquemal and K. D. Jordan, Theo. Chem. Acc., 2012, 131, 1207 (Special Issue From Quantum Mechanics to Force Fields)[PDF][HAL]
DOI: 10.1007/s00214-012-1207-x - Unraveling Low Barrier Hydrogen Bonds in complex systems using a simple quantum topological criterion.
R. Chaudret, G. A. Cisneros, O. Parisel, J-P. Piquemal, Chem. Eur. J.(Communication), 2011, 17, 2833.[PDF][HAL]
DOI: 10.1002/chem.201002978 - Spin-driven activation of dioxygen in various metalloenzymes and their inspired models.
A. de la Lande, D. R. Salahub, J. Maddaluno, A. Scemama, J. Pilme, O. Parisel, H. Gerard, M. Caffarel, J-P Piquemal, J. Comput. Chem. (Rapid Communication), 2011, 32, 1178.[PDF] [HAL]
DOI: 10.1002/jcc.21698 - NCIPLOT: a program for plotting non-covalent interaction regions.
J. Contreras-Garcia, E. R. Johnson, S. Keinan, R. Chaudret, J-P. Piquemal, D. Beratan, W. Yang, J. Chem. Theory. Comput., 2011, 7, 625. [PDF][HAL] [PMC Free Text]
DOI: 10.1021/ct100641a
NCIPLOT PROGRAM: DOWNLOAD - Electron Pair Localization Function (EPLF) for Density Functional Theory and ab initio wave function-based methods : a new tool for chemical interpretation.
A. Scemama, R. Chaudret, M. Caffarel, J-P. Piquemal, J. Chem. Theor. Comput., 2011, 7, 618.[PDF][HAL]
DOI: 10.1021/ct1005938
EPLF PROGRAM: DOWNLOAD - Many-body Exchange-Repulsion in Polarizable Molecular Mechanics. I. Orbital based approximations and application to hydrated metal cations complexes.
R. Chaudret, N. Gresh, O. Parisel, J-P. Piquemal, J. Comput. Chem., 2011, 32, 2949. [PDF][HAL]
DOI: 10.1002/jcc.21865 - Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations.
R. Chaudret, J-P. Piquemal, G. A. Cisneros, Phys. Chem. Chem. Phys., 2011, 13, 11239 [PDF][HAL]
DOI: 10.1039/c0cp02550j - Polarizable water molecules in ligand-metalloprotein recognition. Impact on the relative complexation energies of Zn-dependent phosphomannose isomerase with D-mannose 6-phosphate surrogates.
N. Gresh, B. de Courcy, J.-P. Piquemal, J. Foret, S. Courtiol-Legourd, L. Salmon, J. Phys. Chem. B, 2011, 115, 8304. [PDF][HAL]
DOI: 10.1021/jp2024654 - Enforcing hemidirectionality in Pb(II) complexes: the importance of anionic ligands.
M.-C. van Severen, J.-P. Piquemal, O. Parisel, Chem. Phys. Lett., 2011, 510, 27 [PDF][HAL]
DOI: 10.1016/j.cplett.2011.04.096 - Competitive ligand / chelate binding in [Cu(TMPA)]+ and [Cu(tren)]+ based complexes.
L. Bonniard, S. Ulmer, A. de la Lande, J.-P. Piquemal, O. Parisel, H. Gérard, Cat. Tod., 2011, 177, 79.[PDF][HAL]
DOI: 10.1016/j.cattod.2011.07.015 - Towards 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, C. Clavaguera, N. Gresh, P. Y. Ren, J. Wu, J.-P. Dognon and J.-P. Piquemal, Theo. Chem. Acc., 2012, 131, 1198. [PDF][HAL]
DOI: 10.1007/s00214-012-1198-7
selected to appear in Highlights in Theoretical Chemistry, Vol. 3, 2012, Series Editors: Cramer, Christopher J., Truhlar, Donald G., Springer. [Link]
DOI: 10.1007/ - Toward a ligand specific of Pb2+ with respect to the Zn2+ and Ca2+ cations: A track from quantum chemistry.
M.-C. van Severen, R. Chaudret, O. Parisel, J.-P. Piquemal, Chem. Phys. Lett., 2012, 532, 9 (COVER) [PDF][HAL]
DOI: 10.1016/j.cplett.2012.02.037 - Modeling Structural Coordination and Ligand Binding in Zinc Proteins with the AMOEBA Polarizable Potential.
J. Zhang, W. Yang, J.-P. Piquemal, P. Ren, J. Chem. Theo. Comput., 2012, 8, 1314[PDF] [HAL][PMC Free Text]
DOI: 10.1021/ct200812y - Coupling quantum interpretative techniques: another look at chemical mechanisms in organic reactions.
N. Gillet, R. Chaudret, J. Contreras-Garcia, W. Yang, B. Silvi and J.-P. Piquemal, J. Chem. Theory. Comput., 2012, 8, 3993 [PDF] [HAL][PMC free Text]
DOI: 10.1021/ct300234g - Ionic interactions: comparative topological approach.
J. Contreras-Garcia, M. Calatayud, J.-P. Piquemal and J.M. Recio, Comp. Theo. Chem., 2012, 998, 193.[PDF][HAL]
DOI: 10.1016/j.comptc.2012.07.043 - 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, PY Ren, JC Wu, O Parisel, J-P Piquemal, AIP Conf. Proc., 2012, 1504, 699 [PDF][HAL]
DOI: 10.1063/1.4771791 - Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds?
K. El Hage, J.-P. Piquemal, Z. Hobaika, R. G. Maroun, N. Gresh, J. Comput. Chem., 2013, 34, 1125 [PDF][HAL]
DOI:10.1002/jcc.23242 - Towards Energy Decomposition Analysis for open and closed shell f-elements mono aqua complexes.
A. Marjolin, C. Gourlaouen, C. Clavaguera, J.-P. Dognon, J.-P. Piquemal, Chem. Phys. Lett., 2013, 563, 25 [PDF][HAL]
DOI:10.1016/j.cplett.2013.01.066 - Understanding Structure and Electronic Properties of Th4+ – Water Complexes.
C. Gourlaouen, C. Clavaguera, A. Marjolin, J.-P. Piquemal, J.-P. Dognon , Can. J. Chem., 2013, 91, 821-831.[PDF][HAL]
DOI: 10.1139/cjc-2012-0546 - Further refinements of next-generation force-fields: non empirical localization of off-centered-points in molecules.
R. Chaudret, N. Gresh, G. A. Cisneros, A. Scemama, J-P. Piquemal, Can. J. Chem., 2013, 91, 804-810.[PDF][HAL]
DOI: 10.1139/cjc-2012-0547 - Understanding the chemistry of lead at a molecular level: the Pb(II) 6s6p lone pair can be bisdirected in proteins.
M.-C. van Severen, U. Ryde, O. Parisel, J.-P. Piquemal, J. Chem. Theory. Comput., 2013, 9, 2416-2424[PDF][HAL]
DOI: 10.1021/ct300524v - Towards a Deeper understanding of Enzyme Reactions using the coupled ELF/NCI Analysis: Application to DNA repair enzymes.
D. Fang, R. Chaudret, J.-P. Piquemal, G. A. Cisneros, J. Chem. Theory. Comput. 2013, 9, 2156-2160.[PDF][HAL]
DOI: 10.1021/ct400130b - Are bond critical points really critical for hydrogen bonding?
J. R. Lane, J. Contreras-Garcia, J.-P. Piquemal, B. J. Miller, H. G. Kjaergaar, J. Chem. Theory Comput., 2013, 9, 3263 [PDF][HAL]
DOI: 10.1021/ct400420r - Unravelling Non Covalent Interactions within Flexible Biomolecules: from electron density topology to gas phase spectroscopy.
R. Chaudret, B. de Courcy,J. Contreras-Garcia, E. Gloaguen, A. Zehnacker-Rentien, M. Mons, J.-P. Piquemal, Phys. Chem. Chem. Phys., 2014, 16, 9876, [PDF][HAL]
DOI: 10.1039/C3CP52774C - La surface d’energie potentielle vue par les champs de forces
I. Demachy, J.-P. Piquemal, l’Actualité Chimique, 2014, 388-389, 37-42 [PDF][HAL]
[LINK to Journal] - Modeling Organochlorine Compounds and the sigma hole Effect Using a Polarizable Field.
X. Mu, Q. Wang, L.P. Wang, S. D. Fried, J.-P. Piquemal, K. N. Dalby, P. Y. Ren, J. Phys. Chem. B, 2014, 118, 6456-6465 [PDF][HAL][PMC Free Text]
DOI: 10.1021/jp411671a - Quantum Calculations in Solution for Large to Very Large Molecules: a New Linear Scaling QM/Continuum Approach.
F. Lipparini, L. Lagardere, G. Scalmani, B. Stamm, E. Cances, Y. Maday, J.-P. Piquemal, M. Frisch, B. Mennucci, J. Phys. Chem. Lett, 2014, 5, 953-958 [PDF][HAL]
DOI: 10.1021/jz5002506 - GEM*: A Molecular Electronic Density–Based Force Field for Classical Molecular Dynamics Simulations.
R. Duke, O. Starovoytov, J.-P. Piquemal, G. A. Cisneros, J. Chem. Theory Comput., 2014, 10, 1361-1365 [PDF][HAL] (Open Access)
DOI: 10.1021/ct500050p - Scalable evaluation of the polarization energy and associated forces in polarizable molecular dynamics: I. towards massively parallel direct space computations.
F. Lipparini, L. Lagardère, B. Stamm, E. Cancès, M. Schnieders, P. Y. Ren, Y. Maday, J.-P. Piquemal, J. Chem. Theory. Comput., 2014, 10, 1638-1651[HAL][PDF][PMC Free Text]
DOI: 10.1021/ct401096t - Revisiting H2O Nucleation around Au+ and Hg2+: the Peculiar Pseudo-Soft Character of the gold cation.
R. Chaudret, J. Contreras-Garcia, M. Delcey, O. Parisel, W. Yang, J.-P. Piquemal, J. Chem. Theory. Comput., 2014, 10, 1900-1909 [PDF][HAL]
DOI: 10.1021/ct4006135 - DFT steric based energy decomposition analysis of intermolecular interactions.
D. Fang, J.-P Piquemal, J.-P. Piquemal, G.A. Cisneros, S. Liu, TCA, 2014, 133, 1484 [PDF][HAL]
DOI:10.1007/s00214-014-1484-7 - A Supervised Fitting Approach to Force Field Parametrization with Application to the SIBFA Polarizable Force Field.
M. Devereux, N. Gresh, J.-P. Piquemal, M. Meuwly, J. Comput. Chem., 2014, 35, 1577-1591 (COVER) [PDF][HAL]
DOI: 10.1002/jcc.23661 - 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. Lagardère, T. A. Darden, G. A. Cisneros, J-P. Piquemal, J. Phys. Chem. A, 2014, 118, 7598-7612 [HAL] [PDF]
DOI: 10.1021/jp5051657 - Synthesis and structure-activity relationship of non peptidic antagonists of Neuropilin-1 receptor.
W. Q. Liu, V. Megale, L. Borriello, B. Leforban, M. Montès, E. Goldwaser, N. Gresh, J.-P. Piquemal, R. Hadj-Slimane, O. Hermine, C. Garbay, F. Raynaud, Y. Lepelletier, L. Demange, Bioorg Med. Chem. Lett., 2014, 24, 4254-4259 [PDF][HAL]
DOI: 10.1016/j.bmcl.2014.07.028 - Polarizable Molecular Mechanics studies of Cu(I)/Zn(II) Superoxide Dismutase. Bimetallic binding site and structured waters.
N. Gresh, K. Hage, D. Perahia, J-P. Piquemal, C.Berthomieu, D. Berthomieu.,J. Comput. Chem., 2014, 35, 2096-2106 [PDF][HAL]
DOI: 10.1002/jcc.23724 - Characterizing Molecular Interactions in Chemical Systems.
D. Gunther, R. A. Boto, J. Contreras-Garcia, JP. Piquemal, J. Thierny, IEEE Transactions on Visualization and Computer Graphics, 2014, 20, 2476 – 2485. [HAL]
DOI: 10.1109/TVCG.2014.2346403 - Conformational analysis of a polyconjugated protein-binding ligand by joint ab initio quantum chemistry and polarizable molecular mechanics. Addressing the issues of anisotropy, conjugation, polarization, and multipole transferability.
E. Goldwaser, B. de Courcy, L. Demange, C. Garbay, F. Raynaud, R. Hadj-Slimane, J.-P. Piquemal, N. Gresh, J. Mol. Mod., 2014, 20, 2472 [PDF][HAL]
DOI: 10.1007/s00894-014-2472-5 - Hydration Gibbs Free Energies of Open and Closed Shell Trivalent Lanthanide and Actinide Cations from Polarizable Molecular Dynamics.
A. Marjolin, C. Gourlaouen, C. Clavaguera, P. Y. Ren, J.-P. Piquemal, J.-P. Dognon, J. Mol. Mod., 2014, 20, 2471[PDF][HAL]
DOI: 10.1007/s00894-014-2471-6 - 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.
K. El Hage, J.-P. Piquemal, Z. Hobaika, R. G. Maroun, N. Gresh, 2014, J. Phys. Chem. A, 118, 9772-9782 [PDF][HAL]
DOI: 10.1021/jp5079899 - Quantum, Classical and Hybrid QM/MM Calculations in Solution: General Implementation of thE ddCOSMO Linear Scaling Strategy
F. Lipparini, G. Scalmani, L. Lagardère, B. Stamm, E. Cancès, Y. Maday, J-P. Piquemal, M. J. Frisch, B. Mennucci, J. Chem. Phys., 2014, 141, 184108 [PDF][HAL]
DOI: 10.1063/1.4901304 - Could the ‘Janus-like’ properties of the halobenzene CX bond (X=Cl, Br) be leveraged to enhance molecular recognition?
K. El Hage, J.-P. Piquemal, Z. Hobaika, R. G. Maroun, N. Gresh, J. Comput. Chem., 2015, 36, 210-221 (COVER) [PDF][HAL]
DOI: 10.1002/jcc.23786 - Quantum-chemistry based calibration of the alkali metal cation series (Li+ Cs+) for large-scale polarizable molecular mechanics/dynamics simulations.
T. Dudev, M. Devereux,M. Meuwly, C. Lim, J-P. Piquemal, N. Gresh, J. Comput. Chem., 2015, 36, 285-302 (COVER) [PDF][HAL]
DOI: 10.1002/jcc.23801 - Entasis Through Hook-and-Loop Fastening in a Glycoligand with Cumulative Weak Forces Stabilizing CuI.
L. Garcia, F. Cisnetti, N. Gillet, R. Guillot, M. AumontNicaise, J.P. Piquemal, M. Desmadril, F. Lambert, C. Policar., J. Am. Chem. Soc., 2015, 137, 1141-1146 [HAL]
DOI: 10.1021/ja510259p - Polarizable Molecular Dynamics in a Polarizable Continuum Solvent.
F. Lipparini, L. Lagardère, C. Raynaud, B. Stamm, E. Cancès, M. Schnieders, P. Y. Ren, B. Mennucci, Y. Maday, J.-P. Piquemal, J. Chem. Theory. Comput., 2015, 11, 623-634 [HAL][PMC Free Text]
DOI: 10.1021/ct500998q - 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, David Perahia, Christophe Narth, Louis Lagardere, Filippo Lipparini, Jean-Philip Piquemal, 2015, in Quantum Modeling of Complex Molecular Systems, vol. 21, pp 1-49, Editors: J. L. Rivail, M. Ruiz-Lopez and X. Assfeld, Springer.[HAL]
DOI: 10.1007/978-3-319-21626-3_1 - Polarizable Force Fields for Biomolecular Modeling.
Y. Shi, M. Schnieders, P. Y. Ren, J.-P. Piquemal Reviews in Computational Chemistry, 2015, Vol. 28, 51-86, Wiley [HAL]
DOI: 10.1002/9781118889886.ch2 - Bridging Organometallics and Quantum Chemical Topology: Understanding electronic relocalisation during palladium-catalyzed reductive elimination.
B. de Courcy, E. Derat, J.-P. Piquemal, J. Comput. Chem., 2015, 36, 1167-1175 [PDF][HAL]
DOI: 10.1002/jcc.23911 - A General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field.
Q. Wang, J. A. Rackers, C. He, R. Qi, C. Narth, L. Lagardère, N. Gresh, J. W. Ponder, J-P. Piquemal, P. Y. Ren, J. Chem. Theory. Comput. 2015, 11, 2609-2618 [HAL][PMC Free Text]
DOI: 10.1021/acs.jctc.5b00267 - Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald.
L. Lagardère, F. Lipparini, E. Polack, B. Stamm, E. Cancès, M. Schnieders, P. Y. Ren, Y. Maday, J.-P. Piquemal, J.Chem. Theory. Comput., 2015, 11, 2589-2599 [HAL] [PMC Free Text]
DOI: 10.1021/acs.jctc.5b00171 - Approaching the double-faceted nature of the CX bond in halobenzenes with a bifunctional probe.
K. El Hage, J.-P. Piquemal, Z. Hobaika, R. G. Maroun, N. Gresh, Chem. Phys. Lett., 2015, 637, 51-57 [PDF][HAL]
DOI: 10.1016/j.cplett.2015.07.047 - 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, J-P. Piquemal, J. Sponer, J. Phys. Chem. B, 2015, 119, 9477-9495 [HAL][PDF]
DOI: 10.1021/acs.jpcb.5b01695 - Butanethiol adsorption and dissociation on Ag (111): a DFT study.
A. Li, J.-P. Piquemal, J. Richard, M. Calatayud, Surf. Sci., 2016, 646, 247-252 [HAL]
DOI: 10.1016/j.susc.2015.06.009/ - Interpretation of the reduced density gradient.
R. A. Boto, J. Contreras-Garcia, J. Tierny, J- P. Piquemal, Mol. Phys., 2016, 114, 1406-1414. [HAL]
DOI: 10.1080/00268976.2015.1123777 - Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles.
C. Narth, L. Lagardère, E. Polack, N. Gresh, Q. Wang, R. Bell, David, J. Rackers, J. W. Ponder, P. Y. Ren, J.-P. Piquemal ,J. Comput. Chem., 2016, 37, 494-506(COVER) [HAL]
DOI: 10.1002/jcc.24257 - LICHEM: A QM/MM Program for Simulations with Multipolar and Polarizable Force Fields.
E. G. Kratz, A. R. Walker, L. Lagardère, F. Lipparini, J.-P. Piquemal, G. A. Cisneros, J. Comput. Chem., 2016, 37(11), 1019-1029 (COVER).[HAL][PMC Free Text]
DOI: 10.1002/jcc.24295 - A complete NCI perspective: from new bonds to reactivity.
C. Narth, Z. Maroun, R. A. Boto, R. Chaudret, M.-L. Bonnet, J.-P. Piquemal, J. Contreras-Garcia,2016 in Applications of Topological Methods in Molecular Chemistry, Challenges and Advances in Computational Chemistry and Physics series, Edts: Esmail Alikhani, Remi Chauvin, Christine Lepetit, and Bernard Silvi, Springer, p491-527[HAL]
DOI: 10.1007/978-3-319-29022-5_18 - Status of the Gaussian Electrostatic Model a Density-Based Polarizable Force Field.
Jean-Philip Piquemal, G. Andres Cisneros, 2016 in Many-body effects and electrostatics in Biomolecules, Eds. Qiang Cui, Pengyu Ren and Markus Meuwly, chapter 8, p269-299, Pan Standford Publishing, ISBN:9789814613927 [ HAL][PDF][[link]
DOI: 10.1201/b21343-11 - Study of the inhibition mechanism of HIV-1 integrase by diketoacids molecules.
L. El Khoury, Z. Hobaika, K. El Hage, S. Fermandjian, J.-P. Piquemal, N. Gresh, R. G. Maroun, Journal of Virus Eradication, 2016, 2, supplement 1, 14
[Full text] - A QM/MM approach using the AMOEBA polarizable embedding: from ground state energies to electronic excitations.
D. Loco, E. Polack, S. Caprasecca, L. Lagardère, F. Lipparini, J.-P. Piquemal, B. Mennucci, J. Chem. Theory. Comput., 2016, 12, 3654-3661 [HAL]
DOI: 10.1021/acs.jctc.6b00385 - 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.
N. Gresh, D. Perahia, B. de Courcy, J. Foret, C. Roux, L. El-Khoury, J.-P. Piquemal, L. Salmon, J. Comput. Chem., 2016, 37, 2770-2782 [PDF][HAL]
DOI: 10.1002/jcc.24503 - An Optimized Charge Penetration Model for Use with the AMOEBA Force Field.
J. A. Rackers, Q. Wang, J.-P. Piquemal, P. Ren, J. W. Ponder, Phys. Chem. Chem. Phys. (Special issue: Insights from advanced methods in molecular dynamics ), 2017, 19, 276-291 [HAL][PMC Free Text]
DOI: 10.1039/C6CP06017J - Truncated Conjugate Gradient (TCG): an optimal strategy for the analytical evaluation of the many-body polarization energy and forces in molecular simulations.
F. Aviat, A. Levitt, Y. Maday, B. Stamm, P. Y. Ren, J. W. Ponder, L. Lagardere, J.-P.Piquemal, J. Chem. Theory. Comput., 2017, 13, 180-190 (Open Access) [HAL]
DOI: 10.1021/acs.jctc.6b00981 - 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.
N. Gresh, S. Naseem-Khan, L. Lagardère, J.-P. Piquemal, J. E. Sponer, J. Sponer, J. Phys. Chem. B, 2017, 121, 3997-4014 [HAL]
DOI: 10.1021/acs.jpcb.7b01836 - The inhibition process of HIV-1 integrase by diketoacids molecules: understanding the factors governing the better efficiency of dolutegravir.
L. El Khoury, Jean-Philip Piquemal , Serge Fermandjian, Richard G. Maroun, Nohad Gresh, Zeina Hobaika, BBRC, 2017, 488, 433-438 [HAL]
DOI: 10.1016/j.bbrc.2017.05.001 - Importance of explicit smeared lone-pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange-repulsion and charge transfer contributions.
L. El Khoury, S. Naseem-Khan, K. Kwapien, D. Perahia, Z. Hobaika, R. Maroun, J.-P. Piquemal, N. Gresh, J. Comput. Chem., 2017, 38, 1897-1920 [HAL]
DOI: 10.1002/jcc.24830 - Capturing Many-body Interactions with Classical Dipole Induction Models.
C. Liu, R. Qi, Q. Wang, J.-P. Piquemal, P. Ren, J. Chem. Theory. Comput., 2017, 13, 2751-2761 (Open Access)[HAL]
DOI: 10.1021/acs.jctc.7b00225 - Calibration of 1,2,4-Triazole-3-Thione, an Original Zn-Binding Group of Metallo-betaLactamase Inhibitors. Validation of a Polarizable MM/MD Potential by Quantum Chemistry.
K. Kwapien, M. Damergi, S. Nader, L. El Khoury, Z. Hobaika, R. Maroun, J.-P. Piquemal, L. Gavara, D. Berthomieu, J.-F. Hernandez, N. Gresh, J. Phys. Chem. B, 2017, 121, 6295-6312 [PDF][HAL]
DOI: 10.1021/acs.jpcb.7b01053 - Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs.
M. Harger, D. Li, Z. Wang, K. Dalby, L. Lagardère, J.-P. Piquemal, J. Ponder, P. Ren, J. Comput. Chem., 2017, 38, 2047-2055[PDF][HAL][PMC Free Text]
DOI: 10.1002/jcc.24853 - A simple isomerisation of the purine scaffold of a kinase inhibitor, roscovitine, affords a ten- fold enhancement of its affinity for CDK5 and CDK7. Could this be traced back to conjugation-induced stiffenings/loosenings of rotational barriers?
K. El Hage, J.-P. Piquemal, N. Oumata, L. Meijer, H. Galons, N. Gresh, ACS Omega, 2017, 2, 3467-3474 (Open Access)[HAL]
DOI: 10.1021/acsomega.7b00471 - Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding.
D. Loco, L. Lagardère, S. Caprasecca, F. Lipparini, B. Mennucci, J.-P. Piquemal, J. Chem. Theory. Comput, 2017, 13, 4025-4033 (Open Access)[HAL]
DOI: 10.1021/acs.jctc.7b00572 - The Truncated Conjugate Gradient (TCG), a Non-iterative/Fixed-cost Strategy for Computing Polarization in Molecular Dynamics: Fast Evaluation of Analytical Forces.
F. Aviat, L. Lagardère, J.P. Piquemal, J. Chem. Phys., 2017, 147, 161724 (special issue: from Quantum Mechanics to Force fields)[HAL][ArXiv]
DOI: 10.1063/1.4985911 - Preface: Special Topic From Quantum Mechanics to Force Fields.
J.-P. Piquemal, K. D. Jordan, J. Chem. Phys., 2017, 147, 161401 (special issue: from Quantum Mechanics to Force fields)[HAL]
DOI: 10.1063/1.5008887 - Revealing strong interactions with the reduced density gradient: a benchmark for covalent, ionic and charge-shift bonds covalent and non-covalent interactions.
R. Alvarez-Boto, J.-P. Piquemal, J. Contreras-Garcia, TCA, 2017,136, 139(ESCB1 conference special issue) [HAL]
DOI: 10.1007/s00214-017-2169-9 - Towards Scalable and Accurate Molecular dynamics using the SIBFA polarizable force field.
L. Lagardère, L. El-Khoury, S. Nassem-Kahn, F. Aviat, N. Gresh, J.P. Piquemal, AIP Conf. Proc., 2017, 1906, 030018 (Proceedings of the ICCMSE 2017 conference)[PDF][HAL]
DOI: 10.1063/1.5012297 - Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Polarizable Force Fields.
L. Lagardère, L.-H. Jolly, F. Lipparini, F. Aviat, B. Stamm, Z. F. Jing, M. Harger, H. Torabifard, G. A. Cisneros, M. J. Schnieders, N. Gresh, Y. Maday, P. Ren, J. W. Ponder, J.-P. Piquemal, Chem. Sci., 2018, 9, 956-972 (Open Access)[HAL]
DOI: 10.1039/C7SC04531J - Independent Gradient Model: a new approach for probing strong and weak interactions in molecules from wave function calculations.
C. Lefebvre, H. Khartabil, J-C. Boisson, J. Contreras-Garcia, J.-P. Piquemal, E. Henon, Chem. Phys. Chem., 2018, 19, 724-735 [PDF][HAL]
DOI: 10.1002/cphc.201701325 - AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.
C. Zhang, C. Lu, Z. Jing, C. Wu, J-P. Piquemal, J. W. Ponder, P. Ren, J. Chem. Theory. Comput., 2018, 14, 2084–2108 [HAL][PMC-Free Access]
DOI: 10.1021/acs.jctc.7b01169 - AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in its Ferrous and Ferric Forms.
X. Wu , C. Clavaguera , L. Lagardère , J-P. Piquemal, A. de la Lande, J. Chem. Theory. Comput., 2018, 14, 2705–2720.[HAL] [PDF]
DOI: 10.1021/acs.jctc.7b01128 - QM/MM simulations with the Gaussian Electrostatic Model, a density–based polarizable potential.
H. Gökcan, E. Kratz, T. A. Darden, J.-P. Piquemal, G. A. Cisneros, J. Phys. Chem. Lett., 2018, 9 (11), pp 3062–3067.[HAL][PMC Free Text]
DOI: 10.1021/acs.jpclett.8b01412 - Elucidating the phosphate binding mode of PBP: The Critical Effect of Buffer Solution.
R. Qi, Z. Jing, C. Liu, J.-P. Piquemal, K. N. Dalby, P. Ren, J. Phys. Chem. B, 2018, 122(24):6371-6376.[HAL][PMC Free Text]
DOI: 10.1021/acs.jpcb.8b03194 - A coherent derivation of the Ewald summation for arbitrary orders of multipoles: The self-terms.
B. Stamm, L. Lagardère, É. Polack, Yvon Maday, J.-P. Piquemal, J. Chem. Phys., 2018, 149 (12), 124103 [PDF][HAL][ArXiv]
DOI: 10.1063/1.5044541 - Tinker 8: Software Tools for Molecular Design.
J. A. Rackers, Z. Wang, C. Lu, M. L. Maury, L. Lagardère, M. J. Schnieders, J.-P. Piquemal, P. Ren, J. W. Ponder, J. Chem. Theory. Comput., 2018, 14 (10), 5273–5289 [HAL][PMC Free Text][PDF]
DOI: 10.1021/acs.jctc.8b00529 - How to make continuum solvation incredibly fast in a few simple steps: a practicle guide to the domain decomposition paradigm for the Conductor-like Screening Model.
B. Stamm, L. Lagardère, G. Scalmani, P. Gatto, E. Cancès, J.-P. Piquemal, Y. Maday, B. Mennucci, F. Lipparini, Int. J. Quant. Chem., 2019, 119, e25669 [HAL]
DOI: 10.1002/qua.25669 - Polarizable force fields for biomolecular simulations: Recent advances and applications.
Z. Jing, C. Liu, S. Y. Cheng, R. Qi, B. D. Walker, J.-P. Piquemal, P. Ren, Ann. Rev. Biophys, 2019, 48, 371-394 [HAL][PMC Free Text]
DOI:10.1146/annurev-biophys-070317-033349 - Massively parallel implementation of Steered Molecular Dynamics in Tinker-HP: polarizable versus non-polarizable simulations.
F. Célerse, L. Lagardère, E. Derat, J.-P.Piquemal, J. Chem. Theory. Comput., 2019, 15, 3694-3709 [ChemRxiv][HAL]
Erratum: J. Chem. Theory. Comput., 2021, 17, 5, 3235–3236 [HAL][PDF] DOI: 10.1021/acs.jctc.1c00405
DOI: 10.1021/acs.jctc.9b00199 - Pushing the limits of Multiple-Timestep Strategies for Polarizable Point Dipole Molecular Dynamics.
L. Lagardère, F. Aviat, J.-P. Piquemal, J. Phys. Chem. Lett., 2019, 10, 2593−2599 [HAL] [PDF]
DOI: 10.1021/acs.jpclett.9b00901 - Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.
D. Bedrov, J.-P. Piquemal, O. Borodin, A. D. MacKerell Jr, B. Roux, C. Schröder, Chem. Rev., 2019, 119, 7940-7995(Open Access) [HAL][PDF]
DOI: 10.1021/acs.chemrev.8b00763 - AMOEBA+ Classical Potential for Modeling Molecular Interactions.
C. Liu, J.-P. Piquemal, P. Ren, J. Chem. Theory. Comput., 2019, 15, 4122-4139 [ChemRxiv][HAL][PMC Free Text]
DOI: 10.1021/acs.jctc.9b00261 - Towards Large Scale Hybrid QM/MM Dynamics of Complex Systems with Advanced Point Dipole Polarizable Embeddings.
D. Loco, L. Lagardère, G. A. Cisneros, G. Scalmani, M. Frisch, F. Lipparini, B. Mennucci, J.-P. Piquemal, Chem. Sci., 2019, 10, 7200-7211 (Open Access) [HAL]
DOI: 10.1039/C9SC01745C - Grands Challenges: Joliot-Curie.
Various authors (including JPP), Grands Challenges, 2019, GENCI and CEA [PDF][ResearchGate] - Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0].
L. H. Jolly, A. Duran, L. Lagardère, J. W. Ponder, P. Y. Ren, J.-P. Piquemal, Living Journal of Computational Molecular Science, 2019, 1 (2), 10409 (Open Access) [ArXiv][HAL][PDF]
DOI: 10.33011/livecoms.1.2.10409 - Molecular Dynamics using Non-variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model.
P. P. Poier, L. Lagardère, J.-P. Piquemal, F. Jensen, J. Chem. Theory. Comput., 2019, 15, 11, 6213-6224 [ChemrXiv][HAL]
DOI: 10.1021/acs.jctc.9b00721 - Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities.
L. El Khoury, K. El Hage, J.-P. Piquemal, S. Fermandjian, R. G. Maroun, N. Gresh, Z. Hobaika, PeerJ Physical Chemistry, 2019, 1, e6 (Open Access) [HAL]
DOI: 10.7717/peerj-pchem.6 - Accurate biomolecular simulations account for electronic polarization.
J. Melcr, J.-P. Piquemal, Front. Mol. Biosci., 2019, 6, 143 (Open Access) [ArXiv][HAL]
DOI: 10.3389/fmolb.2019.00143 - Implementation of Geometry Dependent Charge Flux into the Polarizable AMOEBA+ Potential.
C. Liu, J.-P. Piquemal, P. Ren, J. Phys. Chem. Lett., 2020, 11, 419-426 [HAL][ChemRxiv][PMC Free Text]
DOI: 10.1021/acs.jpclett.9b03489 - Calibration of the dianionic phosphate group. Validation on the recognition site of the homodimeric enzyme phosphoglucose isomerase.
M. Devillers, J.-P. Piquemal,L. Salmon, N. Gresh, J. Comput Chem., 2020, 41, 8, 839-854.[HAL][PDF]
DOI: 10.1002/jcc.26134 - A New Way for Probing Bond Strength.
J. Klein, H. Khartabil, J.C. Boisson, J. Contreras-Garcia, J.-P. Piquemal, E. Henon, J. Phys. Chem A, 2020, 124 (9), 1850–1860 [HAL]
DOI: 10.1021/acs.jpca.9b09845 - Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein (NCp7) using Extensive Polarizable Force Field Free-Energy Simulations.
L. El Khoury, F. Célerse, Louis Lagardère, L.-.H Jolly, E. Derat, Z. Hobaika, R. G. Maroun, P. Ren, S. Bouaziz, N. Gresh, J.-P. Piquemal, J. Chem. Theory. Comput., 2020, 16 (4), 2013–2020 [HAL][ChemRxiv][PMC Free Text]
DOI: 10.1021/acs.jctc.9b01204 - Quantum-Chemistry based design of halobenzene derivatives with augmented affinities for the HIV-1 viral G4/C16 base-pair.
P. El Darazi, L. El khoury, K. El Hage, R. G. Maroun, Z. Hobaika, J-P. Piquemal, N. Gresh, Front. Chem., 2020, 8, 440 (Open Access) [HAL][ArXiv]
DOI: 10.3389/fchem.2020.00440 - Solvation effects drive the selectivity in Diels-Alder reaction under hyperbaric conditions.
D. Loco, R. Spezia, F. Cartier, I. Chataigner, J.–P. Piquemal, Chem. Comm., 2020, 56, 6632-6635 (COVER) [HAL][ChemRxiv]
DOI: 10.1039/D0CC01938K - NCIPLOT4: fast, robust and quantitative analysis of noncovalent interactions .
R. A. Boto, C. Quan, R. Laplaza, F. Peccati, A. Carbone, J.-P. Piquemal, Y. Maday, J. Contreras-García, J. Chem. Theory. Comput. , 2020, 16, 7, 4150–4158 [HAL][ChemRxiv]
DOI: 10.1021/acs.jctc.0c00063 - Velocity jump processes : an alternative to multi-time-step methods for faster and accurate molecular dynamics simulations.
P. Monmarché, J. Weisman, L. Lagardère, J.-P. Piquemal, J. Chem. Phys., 2020, 153, 024101 [ArXiv] [HAL]
DOI: 10.1063/5.0005060 - NCIPLOT and the analysis of Noncovalent Interactions using the Reduced Density Gradient.
R. Laplaza, F. Peccati, R. A. Boto, C. Quan, A. Carbone, J.-P. Piquemal, Y. Maday, J. Contreras-García, WIREs Comp. Mol. Sci., 2021, 11, e1497 [HAL][PDF]
DOI: 10.1002/wcms.1497 - High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling.
T. Jaffrelot Inizan, F. Célerse, O. Adjoua, D. El Ahdab, L.-H. Jolly, C. Liu, P. Ren, M. Montes, N. Lagarde, L. Lagardère, P. Monmarché, J.-P.Piquemal, Chem. Sci., 2021, 12, 4889 – 4907 (Open Access) [ChemRxiv][HAL]
Simulation data can be found on the MolSSi/Bioexcel website : [Link]
DOI: 10.1039/D1SC00145K - Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems.
O. Adjoua, L. Lagardère, L.-H. Jolly, Arnaud Durocher, Z. Wang, T. Very, I. Dupays, T. Jaffrelot Inizan, F. Célerse, P. Ren, J. Ponder, J-P. Piquemal, J. Chem. Theory. Comput., 2021, 17, 4, 2034–2053 (Open Access) (COVER)[HAL][ArXiv]
DOI: 10.1021/acs.jctc.0c01164 -
Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.
R. A. Corrigan, G. Qi, T. Casavant, A. Thiel, J. Lynn, B. Walker, L. Lagardère, J.-P. Piquemal, J. W. Ponder, P. Ren, M. J. Schnieders, J. Chem. Theory Comput., 2021, 17, 4, 2323–2341, online [HAL][ChemRxiv]
DOI: 10.1021/acs.jctc.0c01286 - Assessment of SAPT and Supermolecular EDAs Approaches for the Development of Separable and Polarizable force fields.
S. Naseem-Khan, N. Gresh, A. Misquitta, J.-P.Piquemal, J. Chem. Theory Comput. , 2021, 17, 5, 2759–2774 [HAL][ArXiv]
DOI: 10.1021/acs.jctc.0c01337 - Atomistic Polarizable embeddings: energy, dynamics, spectroscopy and reactivity.
D. Loco, L. Lagardère, O. Adjoua, J.-P. Piquemal, Acc. Chem. Res., 2021, 54, 13, 2812–2822 (Open Access) (COVER)[HAL]
DOI: 10.1021/acs.accounts.0c00662 - Interfacial Water Many-body Effects Drive Structural Dynamics and Allosteric interactions in SARS-CoV-2 Main Protease Dimerization Interface.
D. El Ahdab, L. Lagardère, T. Jaffrelot Inizan, F. Célerse, C. Liu, O. Adjoua, L.H. Jolly, N. Gresh, Z. Hobaika, P. Ren, R. G. Maroun, J.-P. Piquemal, J. Phys. Chem. Lett., 2021, 12, 6218–6226 (COVER) [HAL][ChemRxiv] (Open Access via PMC)
DOI: 10.1021/acs.jpclett.1c01460 - Nuclear Quantum Effects in liquid water at near classical computational cost using the adaptive Quantum Thermal Bath.
N. Mauger, T. Plé, L. Lagardère, S. Bonella, E. Mangaud, J.-P. Piquemal, S. Huppert, J. Phys. Chem. Lett., 2021, 12, 34, 8285–8291 [ArXiv] [HAL]
DOI: 10.1021/acs.jpclett.1c01722 - Improvement of the Gaussian Electrostatic Model by Separate Fitting of Coulomb and Exchange-Repulsion Densities and Implementation of a new Dispersion term.
S. Naseem-Khan,J.-P. Piquemal, G. A. Cisneros, J. Chem. Phys., 2021, 155, 194103 [ChemRxiv][HAL][PMC]
DOI: 10.1063/5.0072380 - On the Quantum Chemical Nature of Lead(II) “Lone Pair”.
C. Gourlaouen, J.-P. Piquemal, Molecules, 2022, 27(1), 27 (Open Access) [HAL][Arxiv]
DOI: 10.3390/molecules27010027 - 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, Y. Miao, E. Derat, J.-P. Piquemal, J. Chem. Theory Comput., 2022, 18, 2, 968–977 (COVER)[HAL][ChemRxiv]
DOI: 10.1021/acs.jctc.1c01024 - O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems.
P. P. Poier, L. Lagardère, J.-P. Piquemal, J. Chem. Theory Comput., 2022, 18, 3, 1633–1645 (COVER)[HAL][ChemRxiv]
DOI: 10.1021/acs.jctc.1c01291 - Computationally driven discovery of SARS-CoV-2 Mpro inhibitors: from design to experimental validation.
L. El Khoury, Z. Jing, A. Cuzzolin, A. Deplano, D. Loco, B. Sattarov, F. Hédin, S. Wendeborn, C. Ho, D. El Ahdab, T. Jaffrelot Inizan, M. Sturlese, A. Sosic, M. Volpiana, A. Lugato, M. Barone, B. Gatto, M. Ludovica Macchia, M. Bellanda, R. Battistutta, C. Salata, I. Kondratov, R. Iminov, A. Khairulin, Y. Mykhalonok, A. Pochepko, V. Chashka-Ratushnyi , I. Kos, S. Moro, M. Montes, P. Ren, J. W. Ponder,L. Lagardère, J.-P. Piquemal, D. Sabbadin, Chem. Sc., 2022, 13, 3674-3687 (Open Access) (COVER)[HAL][ArXiv]
DOI: 10.1039/D1SC05892D - Accurate Deep Learning-aided Density-free Strategy for Many-Body Dispersion-corrected Density Functional Theory.
P. P. Poier, T. Jaffrelot Inizan, O. Adjoua, L. Lagardère, J.-P. Piquemal, J. Phys. Chem. Lett., 2022, 13, 19, 4381–4388 [HAL] [ArXiv]
DOI: 10.1021/acs.jpclett.2c00936 - Development of the Quantum Inspired SIBFA Many-Body Polarizable Force Field: I. Enabling Condensed Phase Molecular Dynamics Simulations.
S. Naseem Kahn, L. Lagardère, C. Narth, G. A. Cisneros, P. Ren, N. Gresh, J.-P. Piquemal, 2022, 18, 6, 3607–3621 [HAL][ArXiv]
DOI: 10.1021/acs.jctc.2c00029 - Efficient and Accurate Description of Diels-Alder Reactions using Density Functional Theory.
D. Loco, I. Chataignier, J.-P. Piquemal, R. Spezia, ChemPhysChem, 2022, e202200349 (Open Access) [HAL][ChemRxiv]
DOI: 10.1002/cphc.202200349 - Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators .
K. El Hage, G. Ribaudo , L. Lagardère, A. Ongaro, P. H. Kahn, L. Demange, J.-P. Piquemal, G. Zagotto, N. Gresh, JCIM, 2022, online [HAL][ArXiv]
DOI: 10.1021/acs.jcim.2c00337 - Polarizable Multiscale Dynamics for probing solvent and complex environments.
D. Loco, J.-P Piquemal in Photochemistry, 2022, 50, 382–398, Editors: Stefano Crespi, Stefano Protti [HAL]
DOI:10.1039/9781839167676-00386 - Improving Condensed Phase Water Dynamics with Explicit Nuclear Quantum Effects: the Polarizable Q-AMOEBA Force Field.
N. Mauger, T. Plé, L. Lagardère, S. Huppert, J.-P. Piquemal, J. Phys. Chem. B, 2022, 126, 43, 8813–8826 [HAL][ArXiv]
DOI: 10.1021/acs.jpcb.2c04454 - Calculating the ground state energy of benzene under spatial deformations with noisy quantum computing.
W. Sennane, J.-P. Piquemal, M. J. Rančić, Phys. Rev. A, 2023, 107, 012416 [HAL][ArXiv]
DOI: 10.1103/PhysRevA.107.012416 - Generalized Many-Body Dispersion Correction through Random-phase Approximation for Chemically Accurate Density Functional Theory.
P. P. Poier, L. Lagardère, J.-P. Piquemal, J. Phys. Chem. Lett., 2023, 14, 6, 1609–1617 (Open Access) [HAL][ArXiv]
DOI: 10.1021/acs.jpclett.2c03722 - Routine Molecular Dynamics Simulations Including Nuclear Quantum Effects: from Force Fields to Machine Learning Potentials.
T. Plé, N. Mauger, O. Adjoua,T. Jaffrelot-Inizan, L. Lagardère, S. Huppert, J.-P. Piquemal, J. Chem. Theory. Comput., 2023, 19, 5, 1432–1445 (COVER) [HAL][ArXiv]
DOI: 10.1021/acs.jctc.2c01233 - Open Source Variational Quantum Eigensolver Extension of the Quantum Learning Machine (QLM) for Quantum Chemistry.
M. Haidar, M. J. Rančić, T. Ayral, Y. Maday, J.-P. Piquemal, WIREs Comp. Mol. Sci., 2023, e1664 (Open Access) [HAL][ArXiv]
DOI: 10.1002/wcms.1664 - Extension of the Trotterized Unitary Coupled Cluster to Triple Excitations.
M. Haidar, M. J. Rančić, Y. Maday, J.-P. Piquemal, J. Phys. Chem. A, 2023, 127, 15, 3543–3550 [HAL][ArXiv]
DOI: 10.1021/acs.jpca.3c01753 - Scalable Hybrid Deep Neural Networks/Polarizable Potentials Biomolecular Simulations including long-range effects.
T. Jaffrelot Inizan, T. Plé, O. Adjoua, P. Ren, H. Gökcan, O. Isayev, L. Lagardère, J.-P. Piquemal, Chem. Sci., 2023, 14, 5438-5452 (Open Access) [HAL][ArXiv]
DOI: 10.1039/D2SC04815A - ANKH: A Generalized O(N) Interpolated Ewald Strategy for Molecular Dynamics Simulations.
I. Chollet, L. Lagardère, J.-P. Piquemal, J. Chem. Theory. Comput., 2023, 19, 10, 2887–2905 [HAL][ArXiv]
DOI: 10.1021/acs.jctc.3c00015 - Polarizable QM/MM description of properties and processes of embedded molecules: from response theory to ab-initio molecular dynamics
M. Nottoli, M. Bondanza, P. Mazzeo, L. Cupellini, C. Curutchet, Daniele Loco, Louis Lagardère, J.-P. Piquemal, B. Mennucci, F. Lipparini, WIREs Comp. Mol. Sci., 2023, e1674 (Open Access) [HAL]
DOI: 10.1002/wcms.1674 - Overlap-ADAPT-VQE: Practical Quantum Chemistry on Quantum Computers via Overlap-Guided Compact Ansätze
C. Feniou, M. Hassan, D. Traoré, E. Giner, Y. Maday, J.-P. Piquemal, Commun. Phys., 2023, 6, 192 (Open Access) [HAL][ArXiv][PDF]
DOI: 10.1038/s42005-023-01312-y
Blog: Check our “Behind the paper” post on the Nature Physics community [LINK]
Selected in the Editor’s Highlights – Communications Physics - Force-Field-Enhanced Neural Network Interactions: from Local Equivariant Embedding to Atom-in-Molecule properties and long-range effects.
T. Plé, L. Lagardère, J.-P. Piquemal, Chem. Sci., 2023, 14, 12554-12569 (Open Access) [HAL][ArXiv]
DOI: 10.1039/D3SC02581K - Smooth Particle Mesh Ewald-integrated stochastic Lanczos Many-body Dispersion algorithm.
P. P. Poier, L. Lagardère, J.-P. Piquemal, J. Chem. Phys., 2023, 159, 15, 154109 [HAL][ArXiv]
DOI: 10.1063/5.0166476 - Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-Polarizable Force Fields.
J. Nochebuena, J.-P. Piquemal, S. Liu, G. A. Cisneros, J. Chem. Theory. Comput., 2023, 19, 21, 7715–7730 [HAL][ChemRxiv]
DOI: 10.1021/acs.jctc.3c00762 - Enforcing local DNA kinks by sequence-selective trisintercalating oligopeptides of a tricationic porphyrin. A polarizable Molecular Dynamics study.
N. Gresh, K. El Hage, L. Lagardère, F. Brégier, J. Godard, J.-P. Piquemal, M. Perrée-Fauvet, V. Sol, ChemPhysChem, 2023, e202300776 [HAL][BioRxiv]
DOI: 10.1002/cphc.202300776 - ReaxFF Simulations of Self-Assembled Monolayers on Silver Surfaces and Nanocrystals.
A. Lahouari, J.-P. Piquemal, J. Richardi, J. Phys. Chem. C, 2024, 128, 3, 1193–1201 [HAL][ArXiv]
DOI: 10.1021/acs.jpcc.3c07098 - Unveiling the Full Dynamical and Reactivity Profiles of Acetylcholinesterase: A Comprehensive All-Atom Investigation.
F. Célerse, L. Lagardère, Y. Bouchibti, F. Nachon, L. Verdier, J.–P. Piquemal, E. Derat, ACS Catalysis, 2024, 14 (3), 1785-1796 [HAL][ChemRxiv]
DOI: 10.1021/acscatal.3c05560 - Incorporating Neural Networks into the AMOEBA Polarizable Force Field.
X. Wang, T. Jaffrelot Inizan, C. Liu, J.-P. Piquemal, P. Ren, J. Phys. Chem. B, 2024, 128 (10), 2381–2388 [HAL][ChemRxiv]
DOI: 10.1021/acs.jpcb.3c08166 - Sparse Quantum State Preparation for Strongly Correlated Systems.
C. Feniou, O. Adjoua, B. Claudon, J. Zylberman, E. Giner, J.-P. Piquemal, J. Phys. Chem. Lett., 2024, 15 (11), 3197–3205 (COVER) [HAL][ArXiv]
DOI: 10.1021/acs.jpclett.3c03159 - Lambda-ABF: Simplified, Accurate and Cost-effective Alchemical Free Energy Computations.
L. Lagardère, L. Maurin, O. Adjoua, K. El Hage, P. Monmarché, J.-P. Piquemal, J. Hénin, J. Chem. Theory. Comput., 2024, 20 (11), 4481-4498 [HAL][ArXiv]
DOI: 10.1021/acs.jctc.3c01249 - Advancing Force Fields Parameterization: A Directed Graph Attention Networks Approach
G. Chen, T. Jaffrelot Inizan, T. Plé, L. Lagardère, J.-P. Piquemal, Y. Maday, J. Chem. Theory. Comput., 2024, 20 (13), 5558-5569 [HAL][ChemRxiv]
DOI: 10.1021/acs.jctc.3c01421 - Force Field X: A Computational Microscope to Study Genetic Variation and Organic Crystals Using Theory and Experiment
R. Gogal, A. Nessler, A. Thiel, H. Bernabe, R. Corrigan Grove, L. Cousineau, J. Litman, J. Miller, G. Qi, M. Speranza, M. Tollefson, T. Fenn, J. Michaelson, O. Okada, J.-P. Piquemal, J. Ponder, J. Shen, R. Smith, W. Yang, P. Ren, M. Schnieders, J. Chem. Phys., 2024, 161, 1, 012501 [HAL][PDF]
DOI: 10.1063/5.0214652 - Polylogarithmic-depth controlled-NOT gates without ancilla qubits.
B. Claudon, J. Zylberman, C. Feniou, F. Debbasch, A. Peruzzo, J.-P. Piquemal, Nat. Commun., 2024, 15, 5886 (Open Access) [HAL][ArXiv]
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Blog: Check our “Behind the paper” post on the Nature Physics community [LINK] - FeNNol: an Efficient and Flexible Library for Building Force-field-enhanced Neural Network Potentials.
T. Plé, O. Adjoua, L. Lagardère, J.-P. Piquemal, J. Chem. Phys., 2024, 161, 4, 042502 [HAL][ArXiv]
DOI: 10.1063/5.0217688 - Water-Glycan Interactions Drive the SARS-CoV-2 Spike Dynamics: Insights into Glycan-Gate Control and Camouflage Mechanism.
M. Blazhynska, L. Lagardère, C. Liu, O. Adjoua, P. Ren, J.-P. Piquemal, Chemical Science, 2024, 15, 14177-14187 (Open Access) (COVER)[HAL][BiorXiv]
DOI: 10.1039/D4SC04364B
=>This article is part of the themed collection: 2024 Chemical Science HOT Article Collection - Leveraging Analog Quantum Computing with Neutral Atoms for Solvent Configuration Prediction in Drug Discovery.
M. D’Arcangelo, L.-Paul. Henry, L. Henriet, D. Loco, N. Gouraud, S. Angebault, J. Sueiro, J. Forêt, P. Monmarché, J.-P. Piquemal, Physical Review Research, 2024, 6, 043020 (Open Access) [HAL][ArXiv]
DOI: 10.1103/PhysRevResearch.6.043020 - Shortcut to Chemically Accurate Quantum Computing via Density-based Basis-set Correction.
D. Traore, O. Adjoua, C. Feniou, I.-M. Lygatsika, Y. Maday, E. Posenitskiy, K. Hammernik, A. Peruzzo, J. Toulouse, E. Giner, J.-P. Piquemal, Commun. Chem., 2024, 7, 269 (Open Access) [HAL][ArXiv]
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Blog: Check our “Behind the paper” post on the Nature Physics community [Link] - High-resolution Molecular Dynamics Simulations of the Pyruvate Kinase Muscle Isoform 1 and 2 (PKM1/2).
Q. Delobelle, T. Jaffrelot Inizan, O. Adjoua, L. Lagardère, F. Célerse, V. Maréchal, J.-P. Piquemal, Chem. Eur. J., 2024, e202402534 [HAL][BioArXiv]
DOI: 10.1002/chem.202402534 - Dynamic pre-structuration of lipid nanodomain-segregating remorin proteins.
Z. Xu, A. Schahl, M.-D. Jolivet, A. Legrand, A. Grélard, M. Berbon, E. Morvan, L. Lagardère, J.-P. Piquemal, A. Loquet, V. Germain, M. Chavent, S. Mongrand, B Habenstein, Commun. Bio., 2024, 7, 1620 (Open Access) [HAL][ResearschSquare]
DOI: 10.1038/s42003-024-07330-y - Histidine 73 methylation coordinates beta-actin plasticity in response to key environmental factors.
A. Schahl, L. Lagardère, B. Walker, P. Ren, A. Jégoud, M. Chavent, J.-P. Piquemal, Nat Commun, 2025, in press (Open Access) [HAL][BioarXiv]
DOI: 10.1101/2022.12.16.520803 - The need to implement FAIR principles in biomolecular simulations.
Rommie Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, Daniel Beltran, Philip C Biggin, Massimiliano Bonomi, Gregory R Bowman, Richard Bryce, Giovanni Bussi, Paolo Carloni, David Case, Andrea Cavalli, Chie-En A Chang, Thomas E Cheatham III, Margaret S Cheung, Cris Chipot, Lillian T Chong, Preeti Choudhary, Cecilia Clementi, Rosana Collepardo-Guevara, Peter Coveney, T Daniel Crawford, Matteo Dal Peraro, Bert de Groot, Lucie Delemotte, Marco De Vivo, Jonathan Essex, Franca Fraternali, Jiali Gao, Josep Lluís Gelpí, Francesco Luigi Gervasio, Fernando Danilo Gonzalez-Nilo, Helmut Grubmüller, Marina Guenza, Horacio V Guzman, Sarah Harris, Teresa Head-Gordon, Rigoberto Hernandez, Adam Hospital, Niu Huang, Xuhui Huang, Gerhard Hummer, Javier Iglesias-Fernández, Jan H Jensen, Shantenu Jha, Wanting Jiao, Shina Caroline Lynn Kamerlin, Syma Khalid, Charles Laughton, Michael Levitt, Vittorio Limongelli, Erik Lindahl, Kersten Lindorff-Larsen, Sharon Loverde, Magnus Lundborg, Yun Lina Luo, Francisco Javier Luque, Charlotte I Lynch, Alexander MacKerell, Alessandra Magistrato, Siewert J Marrink, Hugh Martin, J Andrew McCammon, Kenneth Merz, Vicent Moliner, Adrian Mulholland, Sohail Murad, Athi N Naganathan, Shikha Nangia, Frank Noe, Agnes Noy, Julianna Oláh, Megan O’Mara, Mary Jo Ondrechen, José N Onuchic, Alexey Onufriev, Silvia Osuna, Anna R Panchenko, Sergio Pantano, Michele Parrinello, Alberto Perez, Tomas Perez-Acle, Juan R Perilla, B Montgomery Pettitt, Adriana Pietropalo, Jean-Philip Piquemal, Adolfo Poma, Matej Praprotnik, Maria J Ramos, Pengyu Ren, Nathalie Reuter, Adrian Roitberg, Edina Rosta, Carme Rovira, Benoit Roux, Ursula Röthlisberger, Karissa Y Sanbonmatsu, Tamar Schlick, Alexey K Shaytan, Carlos Simmerling, Jeremy C Smith, Yuji Sugita, Katarzyna Świderek, Makoto Taiji, Peng Tao, Julian Tirado-Rives, Inaki Tunón, Marc W Van Der Kamp, David Van der Spoel, Sameer Velankar, Gregory A Voth, Rebecca Wade, Ariel Warshel, Valerie Vaissier Welborn, Stacey Wetmore, Chung F Wong, Lee-Wei Yang, Martin Zacharias, Modesto Orozco, 2025, in revision [HAL][ArXiv]
DOI: 10.48550/arXiv.2407.16584 - Greedy Gradient-free Adaptive Variational Quantum Algorithms on a Noisy Intermediate Scale Quantum Computer.
C. Feniou, B. Claudon, M. Hassan, A. Courtat, O. Adjoua, Y. Maday, J.-P. Piquemal, 2025, in revision [HAL][ArXiv][PDF]
DOI: 10.48550/arXiv.2306.17159 - Polarizable models for selected Endocrine Disrupting Chemicals and their hosts. A. H. Mazurek, V. Thirion, Ł. Szeleszczuk, J.-P. Piquemal, C. Clavaguera, T. Simonson, 2025, in revision [HAL][ArXiv]
DOI: - Fully-polarizable KS-DFT/AMOEBA embedding scheme for plane wave basis sets through the MiMiC framework.
S. Kvedaravičiūtė, A. Antalík, O. Adjoua, T. Plé, L. Lagardère,U. Rothlisberger, J.-P. Piquemal, J. M. Haugaard Olsen, 2025, submitted [HAL][ChemRXiv]
DOI: 10.26434/chemrxiv-2024-6sp7h - Non-Iterative Disentangled Unitary Coupled-Cluster based on Lie-algebraic structure.
M. Haidar, O. Adjoua, S. Baddredine, A. Peruzzo, J.-P. Piquemal, 2025, in revision [HAL][ArXiv]
DOI: 10.48550/arXiv.2408.14289 - AMOEBA Polarizable Molecular Dynamics Simulations of Guanine Quadruplexes: from the c-Kit Proto-oncogene to HIV-1.
D. S. El Ahdab, L. Lagardère, Z. Hobaika, T. Jaffrelot Inizan, F. Célerse, N. Gresh, R. G. Maroun, J.-P. Piquemal, 2025, in revision [HAL][BioRxiv]
DOI: 10.1101/2024.08.28.610081 - Targeting RNA with Small Molecules using State-of-the-Art Methods Provides Highly Predictive Affinities of Riboswitch Inhibitors.
N. Ansari, C. Liu, F. Hédin, J. Hénin, J. W. Ponder, P. Ren, J.-P. Piquemal, L. Lagardère, K. El Hage, 2025, submitted [HAL][ChemRxiv][PDF]
DOI: 10.26434/chemrxiv-2024-s2lqq-v2 - TBA
B. Claudon, J.-P. Piquemal, P. Monmarché, 2025, submitted [HAL][ArXiv]
DOI: - Velocity Jumps for Molecular Dynamics .
N. Gouraud, L. Lagardère, O. Adjoua, T. Plé, P. Monmarché, J-P. Piquemal, 2025, submitted [HAL][ArXiv]
DOI: 10.48550/arXiv.2412.15073 - TBA
N. Mauger,T. Plé, O. Adjoua, L. Lagardère, S.Huppert, J.-P. Piquemal, 2025, [HAL][ArXiv]
DOI: - BA
A Lahouari, T. Plé, J. Richardi, J.-P. Piquemal, 2025, [HAL][ArXiv]
DOI:
- Theoretical study of phenol and 2-Aminophenol docking at a model of tyrosinase active site.
-