Jean-Philip Piquemal, PhD/HDR - Publications

Affiliations: 
2004-2006 Laboratory of Structural Biology National Institute of Environmental Health Sciences (NIEHS), Durham, NC, United States 
 2006-2017 Chemistry Université Pierre et Marie Curie, Paris, Île-de-France, France 
 2018- Chemistry Sorbonne Université, Paris, France 
Area:
Theoretical Chemistry
Website:
http://piquemalresearch.com

142 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Loco D, Lagardère L, Cisneros GA, Scalmani G, Frisch M, Lipparini F, Mennucci B, Piquemal JP. Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings. Chemical Science. 10: 7200-7211. PMID 31588288 DOI: 10.1039/c9sc01745c  1
2019 Poier PP, Lagardère L, Piquemal JP, Jensen F. Molecular Dynamics using Non-variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model. Journal of Chemical Theory and Computation. PMID 31557014 DOI: 10.1021/acs.jctc.9b00721  1
2019 Liu C, Piquemal JP, Ren P. AMOEBA+ Classical Potential for Modeling Molecular Interactions. Journal of Chemical Theory and Computation. PMID 31136175 DOI: 10.1021/acs.jctc.9b00261  0.76
2019 Célerse F, Lagardère L, Derat E, Piquemal JP. Massively parallel implementation of Steered Molecular Dynamics in Tinker-HP: comparisons of polarizable and non-polarizable simulations of realistic systems. Journal of Chemical Theory and Computation. PMID 31059250 DOI: 10.1021/acs.jctc.9b00199  1
2019 Lagardère L, Aviat F, Piquemal JP. Pushing the limits of Multiple-Timestep Strategies for Polarizable Point Dipole Molecular Dynamics. The Journal of Physical Chemistry Letters. PMID 31050904 DOI: 10.1021/acs.jpclett.9b00901  1
2019 Jing Z, Liu C, Cheng SY, Qi R, Walker BD, Piquemal JP, Ren P. Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications. Annual Review of Biophysics. PMID 30916997 DOI: 10.1146/annurev-biophys-070317-033349  0.76
2018 Stamm B, Lagardère L, Polack É, Maday Y, Piquemal JP. A coherent derivation of the Ewald summation for arbitrary orders of multipoles: The self-terms. The Journal of Chemical Physics. 149: 124103. PMID 30278683 DOI: 10.1063/1.5044541  1
2018 Rackers JA, Wang Z, Lu C, Laury ML, Lagardere L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW. Tinker 8: Software Tools for Molecular Design. Journal of Chemical Theory and Computation. PMID 30176213 DOI: 10.1021/acs.jctc.8b00529  0.76
2018 Qi R, Jing Z, Liu C, Piquemal JP, Dalby KN, Ren P. Elucidating the Phosphate Binding Mode of PBP: The Critical Effect of Buffer Solution. The Journal of Physical Chemistry. B. PMID 29807433 DOI: 10.1021/acs.jpcb.8b03194  0.76
2018 Gokcan H, Kratz EG, Darden TA, Piquemal JP, Cisneros GA. QM/MM Simulations with the Gaussian Electrostatic Model, A Density-Based Polarizable Potential. The Journal of Physical Chemistry Letters. PMID 29775314 DOI: 10.1021/acs.jpclett.8b01412  1
2018 Lagardère L, Jolly LH, Lipparini F, Aviat F, Stamm B, Jing ZF, Harger M, Torabifard H, Cisneros GA, Schnieders MJ, Gresh N, Maday Y, Ren PY, Ponder JW, Piquemal JP. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chemical Science. 9: 956-972. PMID 29732110 DOI: 10.1039/c7sc04531j  1
2018 Wu X, Clavaguera C, Lagardère L, Piquemal JP, de la Lande A. AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms. Journal of Chemical Theory and Computation. PMID 29630819 DOI: 10.1021/acs.jctc.7b01128  1
2018 Zhang C, Lu C, Jing Z, Wu C, Piquemal JP, Ponder JW, Ren P. AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids. Journal of Chemical Theory and Computation. PMID 29438622 DOI: 10.1021/acs.jctc.7b01169  0.76
2017 El Hage K, Piquemal JP, Oumata N, Meijer L, Galons H, Gresh N. A Simple Isomerization of the Purine Scaffold of a Kinase Inhibitor, Roscovitine, Affords a Four- to Seven-Fold Enhancement of Its Affinity for Four CDKs. Could This Be Traced Back to Conjugation-Induced Stiffenings/Loosenings of Rotational Barriers? Acs Omega. 2: 3467-3474. PMID 30023695 DOI: 10.1021/acsomega.7b00471  1
2017 Lefebvre C, Khartabil H, Boisson JC, Contreras-Garcia J, Piquemal JP, Hénon E. Independent Gradient Model: a new approach for probing strong and weak interactions in molecules from wave function calculations. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 29250908 DOI: 10.1002/cphc.201701325  0.68
2017 Aviat F, Lagardère L, Piquemal JP. The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces. The Journal of Chemical Physics. 147: 161724. PMID 29096518 DOI: 10.1063/1.4985911  1
2017 Piquemal JP, Jordan KD. Preface: Special Topic: From Quantum Mechanics to Force Fields. The Journal of Chemical Physics. 147: 161401. PMID 29096449 DOI: 10.1063/1.5008887  0.96
2017 Loco D, Lagardère L, Caprasecca S, Lipparini F, Mennucci B, Piquemal JP. Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding. Journal of Chemical Theory and Computation. 13: 4025-4033. PMID 28759205 DOI: 10.1021/acs.jctc.7b00572  1
2017 Harger M, Li D, Wang Z, Dalby K, Lagardère L, Piquemal JP, Ponder J, Ren P. Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. Journal of Computational Chemistry. 38: 2047-2055. PMID 28600826 DOI: 10.1002/jcc.24853  1
2017 Kwapien K, Damergi M, Nader S, El Khoury L, Hobaika Z, Maroun RG, Piquemal JP, Gavara L, Berthomieu D, Hernandez JF, Gresh N. 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. The Journal of Physical Chemistry. B. PMID 28574718 DOI: 10.1021/acs.jpcb.7b01053  1
2017 El Khoury L, Naseem-Khan S, Kwapien K, Hobaika Z, Maroun RG, Piquemal JP, Gresh N. 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. PMID 28558168 DOI: 10.1002/jcc.24830  1
2017 Liu C, Qi R, Wang Q, Piquemal JP, Ren P. Capturing Many-body Interactions with Classical Dipole Induction Models. Journal of Chemical Theory and Computation. PMID 28482664 DOI: 10.1021/acs.jctc.7b00225  0.76
2017 El Khoury L, Piquemal JP, Fermandjian S, Maroun RG, Gresh N, Hobaika Z. The inhibition process of HIV-1 integrase by diketoacids molecules: Understanding the factors governing the better efficiency of dolutegravir. Biochemical and Biophysical Research Communications. PMID 28478035 DOI: 10.1016/j.bbrc.2017.05.001  1
2017 Gresh N, Naseem-Khan S, Lagardère L, Piquemal JP, Sponer JE, Sponer J. 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. The Journal of Physical Chemistry. B. 121: 3997-4014. PMID 28363025 DOI: 10.1021/acs.jpcb.7b01836  1
2017 Aviat F, Levitt A, Stamm B, Maday Y, Ren P, Ponder JW, Lagardère L, Piquemal JP. Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations. Journal of Chemical Theory and Computation. 13: 180-190. PMID 28068773 DOI: 10.1021/acs.jctc.6b00981  1
2016 Rackers JA, Wang Q, Liu C, Piquemal JP, Ren P, Ponder JW. An optimized charge penetration model for use with the AMOEBA force field. Physical Chemistry Chemical Physics : Pccp. PMID 27901142 DOI: 10.1039/c6cp06017j  0.76
2016 Gresh N, Perahia D, de Courcy B, Foret J, Roux C, El-Khoury L, Piquemal JP, Salmon L. Complexes of a Zn-metalloenzyme binding site with hydroxamate-containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown. Journal of Computational Chemistry. PMID 27699809 DOI: 10.1002/jcc.24503  1
2016 Loco D, Polack É, Caprasecca S, Lagardère L, Lipparini F, Piquemal JP, Mennucci B. A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations. Journal of Chemical Theory and Computation. 12: 3654-61. PMID 27340904 DOI: 10.1021/acs.jctc.6b00385  1
2016 Narth C, Lagardère L, Polack É, Gresh N, Wang Q, Bell DR, Rackers JA, Ponder JW, Ren PY, Piquemal JP. 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. 37: 494-506. PMID 26814845 DOI: 10.1002/jcc.24257  1
2016 Kratz EG, Walker AR, Lagardère L, Lipparini F, Piquemal JP, Andrés Cisneros G. LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields. Journal of Computational Chemistry. 37: 1019-29. PMID 26781073 DOI: 10.1002/jcc.24295  1
2015 Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP. Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle mesh Ewald. Journal of Chemical Theory and Computation. 11: 2589-99. PMID 26575557 DOI: 10.1021/acs.jctc.5b00171  1
2015 Lipparini F, Lagardère L, Raynaud C, Stamm B, Cancès E, Mennucci B, Schnieders M, Ren P, Maday Y, Piquemal JP. Polarizable molecular dynamics in a polarizable continuum solvent. Journal of Chemical Theory and Computation. 11: 623-34. PMID 26516318 DOI: 10.1021/ct500998q  1
2015 Wang Q, Rackers JA, He C, Qi R, Narth C, Lagardere L, Gresh N, Ponder JW, Piquemal JP, Ren P. General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field. Journal of Chemical Theory and Computation. 11: 2609-2618. PMID 26413036 DOI: 10.1021/acs.jctc.5b00267  1
2015 Gresh N, Sponer JE, Devereux M, de Courcy B, Piquemal JP, Sponer J, Gkionis K. Stacked and H-bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics. The Journal of Physical Chemistry. B. PMID 26119247 DOI: 10.1021/acs.jpcb.5b01695  1
2015 de Courcy B, Derat E, Piquemal JP. Bridging organometallics and quantum chemical topology: Understanding electronic relocalisation during palladium-catalyzed reductive elimination. Journal of Computational Chemistry. 36: 1167-75. PMID 25899703 DOI: 10.1002/jcc.23911  1
2015 Garcia L, Cisnetti F, Gillet N, Guillot R, Aumont-Nicaise M, Piquemal JP, Desmadril M, Lambert F, Policar C. Entasis through hook-and-loop fastening in a glycoligand with cumulative weak forces stabilizing Cu(I). Journal of the American Chemical Society. 137: 1141-6. PMID 25563067 DOI: 10.1021/ja510259p  1
2015 Dudev T, Devereux M, Meuwly M, Lim C, Piquemal JP, Gresh N. Quantum-chemistry based calibration of the alkali metal cation series (Li(+)-Cs(+)) for large-scale polarizable molecular mechanics/dynamics simulations. Journal of Computational Chemistry. 36: 285-302. PMID 25545371 DOI: 10.1002/jcc.23801  1
2015 El Hage K, Piquemal JP, Hobaika Z, Maroun RG, Gresh N. Could the "Janus-like" properties of the halobenzene CX bond (X=Cl, Br) be leveraged to enhance molecular recognition? Journal of Computational Chemistry. 36: 210-21. PMID 25408206 DOI: 10.1002/jcc.23786  1
2015 Boto RA, Contreras-García J, Tierny J, Piquemal JP. Interpretation of the reduced density gradient Molecular Physics. 1-9. DOI: 10.1080/00268976.2015.1123777  1
2015 Lipparini F, Lagardère L, Raynaud C, Stamm B, Cancès E, Mennucci B, Schnieders M, Ren P, Maday Y, Piquemal JP. Polarizable molecular dynamics in a polarizable continuum solvent Journal of Chemical Theory and Computation. 11: 623-634. DOI: 10.1021/ct500998q  1
2015 Wang Q, Rackers JA, He C, Qi R, Narth C, Lagardere L, Gresh N, Ponder JW, Piquemal JP, Ren P. General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field Journal of Chemical Theory and Computation. 11: 2609-2618. DOI: 10.1021/acs.jctc.5b00267  1
2015 Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP. Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Toward Massively Parallel Computations Using Smooth Particle Mesh Ewald Journal of Chemical Theory and Computation. 11: 2589-2599. DOI: 10.1021/acs.jctc.5b00171  1
2015 Li A, Piquemal JP, Richardi J, Calatayud M. Butanethiol adsorption and dissociation on Ag (111): A periodic DFT study Surface Science. DOI: 10.1016/j.susc.2015.06.009  1
2015 El Hage K, Piquemal JP, Hobaika Z, Maroun RG, Gresh N. Approaching the double-faceted nature of the CX bond in halobenzenes with a bifunctional probe Chemical Physics Letters. 637: 51-57. DOI: 10.1016/j.cplett.2015.07.047  1
2015 Gresh N, Chaudret R, David P, Hage KE, Narth C, Goldwaser E, Lagardère L, De Courcy B, Lipparini F, Piquemal JP. Addressing the issues of non-isotropy and non-additivity in the development of quantum chemistry-grounded polarizable molecular mechanics Quantum Modeling of Complex Molecular Systems. 1-49. DOI: 10.1007/978-3-319-21626-3_1  1
2014 Duke RE, Starovoytov ON, Piquemal JP, Cisneros GA. GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 10: 1361-5. PMID 26580355 DOI: 10.1021/ct500050p  1
2014 Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP. 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. 10: 1638-1651. PMID 26512230 DOI: 10.1021/ct401096t  1
2014 Gunther D, Boto RA, Contreras-Garcia J, Piquemal JP, Tierny J. Characterizing Molecular Interactions in Chemical Systems. Ieee Transactions On Visualization and Computer Graphics. 20: 2476-85. PMID 26356961 DOI: 10.1109/TVCG.2014.2346403  0.68
2014 Lipparini F, Lagardère L, Scalmani G, Stamm B, Cancès E, Maday Y, Piquemal JP, Frisch MJ, Mennucci B. Quantum Calculations in Solution for Large to Very Large Molecules: A New Linear Scaling QM/Continuum Approach. The Journal of Physical Chemistry Letters. 5: 953-8. PMID 26270973 DOI: 10.1021/jz5002506  1
2014 Lipparini F, Scalmani G, Lagardère L, Stamm B, Cancès E, Maday Y, Piquemal JP, Frisch MJ, Mennucci B. Quantum, classical, and hybrid QM/MM calculations in solution: general implementation of the ddCOSMO linear scaling strategy. The Journal of Chemical Physics. 141: 184108. PMID 25399133 DOI: 10.1063/1.4901304  1
2014 Goldwaser E, de Courcy B, Demange L, Garbay C, Raynaud F, Hadj-Slimane R, Piquemal JP, Gresh N. Conformational analysis of a polyconjugated protein-binding ligand by joint quantum chemistry and polarizable molecular mechanics. Addressing the issues of anisotropy, conjugation, polarization, and multipole transferability. Journal of Molecular Modeling. 20: 2472. PMID 25367040 DOI: 10.1007/s00894-014-2472-5  1
2014 Marjolin A, Gourlaouen C, Clavaguéra C, Ren PY, Piquemal JP, Dognon JP. Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics. Journal of Molecular Modeling. 20: 2471. PMID 25296890 DOI: 10.1007/s00894-014-2471-6  1
2014 El Hage K, Piquemal JP, Hobaika Z, Maroun RG, Gresh N. 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. The Journal of Physical Chemistry. A. 118: 9772-82. PMID 25230384 DOI: 10.1021/jp5079899  1
2014 Gresh N, El Hage K, Perahia D, Piquemal JP, Berthomieu C, Berthomieu D. Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: bimetallic binding site and structured waters. Journal of Computational Chemistry. 35: 2096-106. PMID 25212748 DOI: 10.1002/jcc.23724  1
2014 Liu WQ, Megale V, Borriello L, Leforban B, Montès M, Goldwaser E, Gresh N, Piquemal JP, Hadj-Slimane R, Hermine O, Garbay C, Raynaud F, Lepelletier Y, Demange L. Synthesis and structure-activity relationship of non-peptidic antagonists of neuropilin-1 receptor. Bioorganic & Medicinal Chemistry Letters. 24: 4254-9. PMID 25091928 DOI: 10.1016/j.bmcl.2014.07.028  1
2014 Devereux M, Gresh N, Piquemal JP, Meuwly M. A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field. Journal of Computational Chemistry. 35: 1577-91. PMID 24965869 DOI: 10.1002/jcc.23661  1
2014 Chaudret R, Gresh N, Narth C, Lagardère L, Darden TA, Cisneros GA, Piquemal JP. 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. The Journal of Physical Chemistry. A. 118: 7598-612. PMID 24878003 DOI: 10.1021/jp5051657  1
2014 Chaudret R, Contreras-Garcia J, Delcey M, Parisel O, Yang W, Piquemal JP. Revisiting H2O Nucleation around Au(+) and Hg(2+): The Peculiar "Pseudo-Soft" Character of the Gold Cation. Journal of Chemical Theory and Computation. 10: 1900-1909. PMID 24860276 DOI: 10.1021/ct4006135  1
2014 Mu X, Wang Q, Wang LP, Fried SD, Piquemal JP, Dalby KN, Ren P. Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field. The Journal of Physical Chemistry. B. 118: 6456-65. PMID 24484473 DOI: 10.1021/jp411671a  1
2014 Chaudret R, de Courcy B, Contreras-García J, Gloaguen E, Zehnacker-Rentien A, Mons M, Piquemal JP. Unraveling non-covalent interactions within flexible biomolecules: from electron density topology to gas phase spectroscopy. Physical Chemistry Chemical Physics : Pccp. 16: 9876-91. PMID 24419903 DOI: 10.1039/c3cp52774c  1
2014 Günther D, Boto RA, Contreras-Garcia J, Piquemal JP, Tierny J. Characterizing molecular interactions in chemical systems Ieee Transactions On Visualization and Computer Graphics. 20: 2476-2485. DOI: 10.1109/TVCG.2014.2346403  1
2014 Lipparini F, Lagardère L, Scalmani G, Stamm B, Cancès E, Maday Y, Piquemal JP, Frisch MJ, Mennucci B. Quantum calculations in solution for large to very large molecules: A new linear scaling QM/continuum approach Journal of Physical Chemistry Letters. 5: 953-958. DOI: 10.1021/jz5002506  1
2014 Duke RE, Starovoytov ON, Piquemal JP, Cisneros GA. GEM*: A molecular electronic density-based force field for molecular dynamics simulations Journal of Chemical Theory and Computation. 10: 1361-1365. DOI: 10.1021/ct500050p  1
2014 Lipparini F, Lagardère L, Stamm B, Cancès E, Schnieders M, Ren P, Maday Y, Piquemal JP. 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. 10: 1638-1651. DOI: 10.1021/ct401096t  1
2014 Fang D, Piquemal JP, Liu S, Cisneros GA. DFT-steric-based energy decomposition analysis of intermolecular interactions Theoretical Chemistry Accounts. 133: 1-14. DOI: 10.1007/s00214-014-1484-7  1
2013 Lane JR, Contreras-García J, Piquemal JP, Miller BJ, Kjaergaard HG. Are Bond Critical Points Really Critical for Hydrogen Bonding? Journal of Chemical Theory and Computation. 9: 3263-6. PMID 26584086 DOI: 10.1021/ct400420r  0.6
2013 Van Severen MC, Ryde U, Parisel O, Piquemal JP. Understanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins. Journal of Chemical Theory and Computation. 9: 2416-24. PMID 26583732 DOI: 10.1021/ct300524v  1
2013 Fang D, Chaudret R, Piquemal JP, Cisneros GA. Toward a Deeper Understanding of Enzyme Reactions Using the Coupled ELF/NCI Analysis: Application to DNA Repair Enzymes. Journal of Chemical Theory and Computation. 9: 2156-60. PMID 26583709 DOI: 10.1021/ct400130b  1
2013 El Hage K, Piquemal JP, Hobaika Z, Maroun RG, Gresh N. Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds? Journal of Computational Chemistry. 34: 1125-35. PMID 23386428 DOI: 10.1002/jcc.23242  1
2013 Chaudret R, Gresh N, Cisneros GA, Scemama A, Piquemal JP. Further refinements of next-generation force fields-Nonempirical localization of off-centered points in molecules Canadian Journal of Chemistry. 91: 804-810. DOI: 10.1139/cjc-2012-0547  1
2013 Gourlaouen C, Clavaguéra C, Marjolin A, Piquemal JP, Dognon JP. Understanding the structure and electronic properties of Th 4+-water complexes Canadian Journal of Chemistry. 91: 821-831. DOI: 10.1139/cjc-2012-0546  1
2013 Lane JR, Contreras-García J, Piquemal JP, Miller BJ, Kjaergaard HG. Are bond critical points really critical for hydrogen bonding? Journal of Chemical Theory and Computation. 9: 3263-3266. DOI: 10.1021/ct400420r  1
2013 Fang D, Chaudret R, Piquemal JP, Cisneros GA. Toward a deeper understanding of enzyme reactions using the coupled ELF/NCI analysis: Application to DNA repair enzymes Journal of Chemical Theory and Computation. 9: 2156-2160. DOI: 10.1021/ct400130b  1
2013 Van Severen MC, Ryde U, Parisel O, Piquemal JP. Understanding the chemistry of lead at a molecular level: The Pb(II) 6s6p lone pair can be bisdirected in proteins Journal of Chemical Theory and Computation. 9: 2416-2424. DOI: 10.1021/ct300524v  1
2013 Marjolin A, Gourlaouen C, Clavaguéra C, Dognon JP, Piquemal JP. Towards energy decomposition analysis for open and closed shell f-elements mono aqua complexes Chemical Physics Letters. 563: 25-29. DOI: 10.1016/j.cplett.2013.01.066  1
2012 Gillet N, Chaudret R, Contreras-Garc?a J, Yang W, Silvi B, Piquemal JP. Coupling quantum interpretative techniques: another look at chemical mechanisms in organic reactions. Journal of Chemical Theory and Computation. 8: 3993-3997. PMID 23185140 DOI: 10.1021/ct300234g  1
2012 Zhang J, Yang W, Piquemal JP, Ren P. Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential. Journal of Chemical Theory and Computation. 8: 1314-1324. PMID 22754403 DOI: 10.1021/ct200812y  1
2012 Chaudret R, De Courcy B, Marjolin A, Van Severen MC, Ren PY, Wu JC, Parisel O, Piquemal JP. Unraveling interactions in large complex systems using quantum chemistry interpretative techniques and new generation polarizable force fields Aip Conference Proceedings. 1504: 699-702. DOI: 10.1063/1.4771791  1
2012 Van Severen MC, Chaudret R, Parisel O, Piquemal JP. Toward a ligand specific of Pb 2+ with respect to the Zn 2+ and Ca 2+ cations: A track from quantum chemistry Chemical Physics Letters. 532: 9-12. DOI: 10.1016/j.cplett.2012.02.037  1
2012 Contreras-García J, Calatayud M, Piquemal JP, Recio JM. Ionic interactions: Comparative topological approach Computational and Theoretical Chemistry. 998: 193-201. DOI: 10.1016/j.comptc.2012.07.043  1
2012 Piquemal JP, Jordan KD. From quantum mechanics to force fields: New methodologies for the classical simulation of complex systems Theoretical Chemistry Accounts. 131: 1-2. DOI: 10.1007/s00214-012-1207-x  1
2012 Marjolin A, Gourlaouen C, Clavaguéra C, Ren PY, Wu JC, Gresh N, Dognon JP, Piquemal JP. 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. 131: 1-14. DOI: 10.1007/s00214-012-1198-7  1
2011 Devereux M, van Severen MC, Parisel O, Piquemal JP, Gresh N. Role of Cation Polarization in holo- and hemi-Directed [Pb(H2O)n](2+) Complexes and Development of a Pb(2+) Polarizable Force Field. Journal of Chemical Theory and Computation. 7: 138-147. PMID 26606227 DOI: 10.1021/ct1004005  1
2011 Scemama A, Caffarel M, Chaudret R, Piquemal JP. 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. 7: 618-24. PMID 26596296 DOI: 10.1021/ct1005938  1
2011 Chaudret R, Gresh N, Parisel O, Piquemal JP. Many-body exchange-repulsion in polarizable molecular mechanics. I. Orbital-based approximations and applications to hydrated metal cation complexes. Journal of Computational Chemistry. 32: 2949-57. PMID 21793002 DOI: 10.1002/jcc.21865  1
2011 Gresh N, de Courcy B, Piquemal JP, Foret J, Courtiol-Legourd S, Salmon L. Polarizable water networks in ligand-metalloprotein recognition. Impact on the relative complexation energies of Zn-dependent phosphomannose isomerase with D-mannose 6-phosphate surrogates. The Journal of Physical Chemistry. B. 115: 8304-16. PMID 21650197 DOI: 10.1021/jp2024654  1
2011 Chaudret R, Piquemal JP, Cisneros GA. Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations. Physical Chemistry Chemical Physics : Pccp. 13: 11239-47. PMID 21566841 DOI: 10.1039/c0cp02550j  1
2011 Contreras-García J, Johnson ER, Keinan S, Chaudret R, Piquemal JP, Beratan DN, Yang W. NCIPLOT: a program for plotting non-covalent interaction regions. Journal of Chemical Theory and Computation. 7: 625-632. PMID 21516178 DOI: 10.1021/ct100641a  1
2011 de la Lande A, Salahub DR, Maddaluno J, Scemama A, Pilme J, Parisel O, Gerard H, Caffarel M, Piquemal JP. Spin-driven activation of dioxygen in various metalloenzymes and their inspired models. Journal of Computational Chemistry. 32: 1178-82. PMID 21387344 DOI: 10.1002/jcc.21698  1
2011 Chaudret R, Cisneros GA, Parisel O, Piquemal JP. Unraveling low-barrier hydrogen bonds in complex systems with a simple quantum topological criterion. Chemistry (Weinheim An Der Bergstrasse, Germany). 17: 2833-7. PMID 21308813 DOI: 10.1002/chem.201002978  1
2011 Roux C, Bhatt F, Foret J, de Courcy B, Gresh N, Piquemal JP, Jeffery CJ, Salmon L. The reaction mechanism of type I phosphomannose isomerases: new information from inhibition and polarizable molecular mechanics studies. Proteins. 79: 203-20. PMID 21058398 DOI: 10.1002/prot.22873  1
2011 Scemama A, Caffarel M, Chaudret R, Piquemal JP. 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. 7: 618-624. DOI: 10.1021/ct1005938  1
2011 Devereux M, Van Severen MC, Parisel O, Piquemal JP, Gresh N. Role of cation polarization in holo- and hemi- directed [Pb(H 2O)n]2+ complexes and development of a Pb 2+ polarizable force field Journal of Chemical Theory and Computation. 7: 138-147. DOI: 10.1021/ct1004005  1
2011 Van Severen MC, Piquemal JP, Parisel O. Enforcing hemidirectionality in Pb(II) complexes: The importance of anionic ligands Chemical Physics Letters. 510: 27-30. DOI: 10.1016/j.cplett.2011.04.096  1
2011 Bonniard L, De La Lande A, Ulmer S, Piquemal JP, Parisel O, Gérard H. Competitive ligand/chelate binding in [Cu(TMPA)] + and [Cu(tren)] + based complexes Catalysis Today. 177: 79-86. DOI: 10.1016/j.cattod.2011.07.015  1
2011 De Courcy B, Dognon JP, Clavaguéra C, Gresh N, Piquemal JP. 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. 111: 1213-1221. DOI: 10.1002/qua.22760  1
2010 Wu JC, Piquemal JP, Chaudret R, Reinhardt P, Ren P. Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field. Journal of Chemical Theory and Computation. 6: 2059-2070. PMID 21116445 DOI: 10.1021/ct100091j  1
2010 Gourlaouen C, Parisel O, Piquemal JP. Importance of backdonation in [M-(CO)]p+ complexes isoelectronic to [Au-(CO)]+. The Journal of Chemical Physics. 133: 124310. PMID 20886935 DOI: 10.1063/1.3491266  1
2010 Gloaguen E, de Courcy B, Piquemal JP, Pilmé J, Parisel O, Pollet R, Biswal HS, Piuzzi F, Tardivel B, Broquier M, Mons M. 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. 132: 11860-3. PMID 20687601 DOI: 10.1021/ja103996q  1
2010 Piquemal JP, Salahub D. Editorial: special issue on quantum mechanical modeling of biological systems. Interdisciplinary Sciences, Computational Life Sciences. 2: 1-2. PMID 20640792 DOI: 10.1007/s12539-010-0001-5  1
2010 de Courcy B, Pedersen LG, Parisel O, Gresh N, Silvi B, Pilmé J, Piquemal JP. 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. 6: 1048-1063. PMID 20419068 DOI: 10.1021/ct100089s  1
2010 de la Lande A, Maddaluno J, Parisel O, Darden TA, Piquemal JP. Study of the docking of competitive inhibitors at a model of tyrosinase active site: insights from joint broken-symmetry/Spin-Flip DFT computations and ELF topological analysis. Interdisciplinary Sciences, Computational Life Sciences. 2: 3-11. PMID 20396590 DOI: 10.1007/s12539-010-0096-8  1
2010 Gresh N, Audiffren N, Piquemal JP, de Ruyck J, Ledecq M, Wouters J. 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. The Journal of Physical Chemistry. B. 114: 4884-95. PMID 20329783 DOI: 10.1021/jp907629k  1
2010 Elking DM, Cisneros GA, Piquemal JP, Darden TA, Pedersen LG. Gaussian Multipole Model (GMM). Journal of Chemical Theory and Computation. 6: 190-202. PMID 20209077 DOI: 10.1021/ct900348b  1
2010 van Severen MC, Piquemal JP, Parisel O. Lead substitution in synaptotagmin: a case study. The Journal of Physical Chemistry. B. 114: 4005-9. PMID 20192256 DOI: 10.1021/jp910131r  1
2010 de Courcy B, Piquemal JP, Garbay C, Gresh N. Polarizable water molecules in ligand-macromolecule recognition. Impact on the relative affinities of competing pyrrolopyrimidine inhibitors for FAK kinase. Journal of the American Chemical Society. 132: 3312-20. PMID 20178314 DOI: 10.1021/ja9059156  1
2009 De Courcy B, Gresh N, Piquemal JP. Importance of lone pair interactions/redistribution in hard and soft ligands within the active site of alcohol dehydrogenase Zn-metalloenzyme: Insights from electron localization function. Interdisciplinary Sciences, Computational Life Sciences. 1: 55-60. PMID 20640819 DOI: 10.1007/s12539-008-0027-0  1
2009 Foret J, de Courcy B, Gresh N, Piquemal JP, Salmon L. Synthesis and evaluation of non-hydrolyzable D-mannose 6-phosphate surrogates reveal 6-deoxy-6-dicarboxymethyl-D-mannose as a new strong inhibitor of phosphomannose isomerases. Bioorganic & Medicinal Chemistry. 17: 7100-7. PMID 19783448 DOI: 10.1016/j.bmc.2009.09.005  1
2009 de la Lande A, Salahub D, Moliner V, Gérard H, Piquemal JP, Parisel O. Dioxygen activation by mononuclear copper enzymes: insights from a tripodal ligand mimicking their Cu(M) coordination sphere. Inorganic Chemistry. 48: 7003-5. PMID 19586039 DOI: 10.1021/ic900567z  1
2009 Chaudref R, Ulmera S, Van Severena MC, Gresh N, Pansela O, Cisnerosd GA, Darden TA, Piquemal JP. Progress Towards Accurate Molecular Modeling of Metal Complexes Using Polarizable Force Fields Aip Conference Proceedings. 1102: 185-192. DOI: 10.1063/1.3108373  1
2009 Severen MCv, Piquemal JP, Parisel O. Beyond holo/hemidirectionality in Pb(II) complexes: Can the valence lone pair be bisdirected? Chemical Physics Letters. 478: 17-19. DOI: 10.1016/j.cplett.2009.07.036  1
2009 Gourlaouen C, Parisel O, Piquemal JP. Trends in ns2 np0 [M(CO)]q+ complexes: From germanium to element 114 (Uuq) Chemical Physics Letters. 469: 38-42. DOI: 10.1016/j.cplett.2008.12.040  1
2009 Reinhardt P, Piquemal JP. New intermolecular benchmark calculations on the water dimer: Sapt and supermolecular post-hartree-fock approaches International Journal of Quantum Chemistry. 109: 3259-3267. DOI: 10.1002/qua.22299  1
2008 Reinhardt P, Piquemal JP, Savin A. Fragment-Localized Kohn-Sham Orbitals via a Singles Configuration-Interaction Procedure and Application to Local Properties and Intermolecular Energy Decomposition Analysis. Journal of Chemical Theory and Computation. 4: 2020-9. PMID 26620475 DOI: 10.1021/ct800242n  1
2008 de Courcy B, Piquemal JP, Gresh N. Energy Analysis of Zn Polycoordination in a Metalloprotein Environment and of the Role of a Neighboring Aromatic Residue. What Is the Impact of Polarization? Journal of Chemical Theory and Computation. 4: 1659-68. PMID 26620173 DOI: 10.1021/ct800200j  1
2008 Cisneros GA, Tholander SN, Parisel O, Darden TA, Elking D, Perera L, Piquemal JP. Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding. International Journal of Quantum Chemistry. 108: 1905-1912. PMID 19606279 DOI: 10.1002/qua.21675  1
2008 Pilmé J, Piquemal JP. Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments. Journal of Computational Chemistry. 29: 1440-9. PMID 18293309 DOI: 10.1002/jcc.20904  1
2008 Gourlaouen C, Gérard H, Piquemal JP, Parisel O. Understanding lead chemistry from topological insights: the transition between holo- and hemidirected structures within the [Pb(CO)n]2+ model series. Chemistry (Weinheim An Der Bergstrasse, Germany). 14: 2730-43. PMID 18232031 DOI: 10.1002/chem.200701265  1
2008 De Courcy B, Piquemal JP, Gresh N. Energy analysis of Zn polycoordination in a metalloprotein environment and of the role of a neighboring aromatic residue. What is the impact of polarization? Journal of Chemical Theory and Computation. 4: 1659-1668. DOI: 10.1021/ct800200j  1
2008 Piquemal JP, Pilmé J, Parisel O, Gérard H, Fourré I, Bergés J, Gourlaouen C, De La Lande A, Van Severen MC, Silvi B. What can be learnt on biologically relevant systems from the topological analysis of the electron localization function? International Journal of Quantum Chemistry. 108: 1951-1969. DOI: 10.1002/qua.21711  1
2007 Piquemal JP, Chevreau H, Gresh N. Toward a Separate Reproduction of the Contributions to the Hartree-Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential. Journal of Chemical Theory and Computation. 3: 824-37. PMID 26627402 DOI: 10.1021/ct7000182  1
2007 Gresh N, Cisneros GA, Darden TA, Piquemal JP. Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. Journal of Chemical Theory and Computation. 3: 1960-1986. PMID 18978934 DOI: 10.1021/ct700134r  1
2007 Cisneros GA, Elking D, Piquemal JP, Darden TA. Numerical fitting of molecular properties to Hermite Gaussians. The Journal of Physical Chemistry. A. 111: 12049-56. PMID 17973464 DOI: 10.1021/jp074817r  1
2007 Miller Jenkins LM, Hara T, Durell SR, Hayashi R, Inman JK, Piquemal JP, Gresh N, Appella E. Specificity of acyl transfer from 2-mercaptobenzamide thioesters to the HIV-1 nucleocapsid protein. Journal of the American Chemical Society. 129: 11067-78. PMID 17705474 DOI: 10.1021/ja071254o  1
2007 Piquemal JP, Chelli R, Procacci P, Gresh N. Key role of the polarization anisotropy of water in modeling classical polarizable force fields. The Journal of Physical Chemistry. A. 111: 8170-6. PMID 17665882 DOI: 10.1021/jp072687g  1
2007 Roux C, Gresh N, Perera LE, Piquemal JP, Salmon L. 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. Journal of Computational Chemistry. 28: 938-57. PMID 17253648 DOI: 10.1002/jcc.20586  1
2007 Piquemal JP, Chevreau H, Gresh N. Toward a separate reproduction of the contributions to the Hartree-Fock and DFT intermolecular interaction energies by polarizable molecular mechanics with the SIBFA potential Journal of Chemical Theory and Computation. 3: 824-837. DOI: 10.1021/ct7000182  1
2006 Piquemal JP, Pilmé J. Comments on the nature of the bonding in oxygenated dinuclear copper enzyme models. Journal of Molecular Structure. 764: 77-86. PMID 17893747 DOI: 10.1016/j.theochem.2006.02.013  1
2006 Cisneros GA, Piquemal JP, Darden TA. Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods. The Journal of Chemical Physics. 125: 184101. PMID 17115732 DOI: 10.1063/1.2363374  1
2006 Piquemal JP, Perera L, Cisneros GA, Ren P, Pedersen LG, Darden TA. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. The Journal of Chemical Physics. 125: 054511. PMID 16942230 DOI: 10.1063/1.2234774  1
2006 Cisneros GA, Piquemal JP, Darden TA. Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions. The Journal of Physical Chemistry. B. 110: 13682-4. PMID 16836309 DOI: 10.1021/jp062768x  1
2006 Gourlaouen C, Piquemal JP, Parisel O. [Pb(H2O)]2+ and [Pb(OH)]+: four-component density functional theory calculations, correlated scalar relativistic constrained-space orbital variation energy decompositions, and topological analysis. The Journal of Chemical Physics. 124: 174311. PMID 16689575 DOI: 10.1063/1.2186994  1
2006 Piquemal JP, Cisneros GA, Reinhardt P, Gresh N, Darden TA. Towards a force field based on density fitting. The Journal of Chemical Physics. 124: 104101. PMID 16542062 DOI: 10.1063/1.2173256  1
2006 Gourlaouen C, Piquemal JP, Saue T, Parisel O. 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 (M(p+) = Cu+, Zn2+, Ag+, Cd2+, Au+, Hg2+). Journal of Computational Chemistry. 27: 142-56. PMID 16312018 DOI: 10.1002/jcc.20329  1
2005 Cisneros GA, Piquemal JP, Darden TA. Intermolecular electrostatic energies using density fitting. The Journal of Chemical Physics. 123: 044109. PMID 16095348 DOI: 10.1063/1.1947192  1
2005 Antony J, Piquemal JP, Gresh N. Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-beta-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry. Journal of Computational Chemistry. 26: 1131-47. PMID 15937993 DOI: 10.1002/jcc.20245  1
2005 Gresh N, Piquemal JP, Krauss M. Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations. Journal of Computational Chemistry. 26: 1113-30. PMID 15934064 DOI: 10.1002/jcc.20244  1
2005 Piquemal JP, Marquez A, Parisel O, Giessner-Prettre C. A CSOV study of the difference between HF and DFT intermolecular interaction energy values: the importance of the charge transfer contribution. Journal of Computational Chemistry. 26: 1052-62. PMID 15898112 DOI: 10.1002/jcc.20242  1
2003 Piquemal JP, Gresh N, Giessner-Prettre C. Improved Formulas for the Calculation of the Electrostatic Contribution to the Intermolecular Interaction Energy from Multipolar Expansion of the Electronic Distribution. The Journal of Physical Chemistry. A. 107: 10353-9. PMID 26313624 DOI: 10.1021/jp035748t  1
2003 Piquemal JP, Williams-Hubbard B, Fey N, Deeth RJ, Gresh N, Giessner-Prettre C. Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF. Journal of Computational Chemistry. 24: 1963-70. PMID 14531050 DOI: 10.1002/jcc.10354  1
2003 Piquemal JP, Maddaluno J, Silvi B, Giessner-Prettre C. Theoretical study of phenol and 2-aminophenol docking at a model of the tyrosinase active site New Journal of Chemistry. 27: 909-913. DOI: 10.1039/b210307a  1
2003 Piquemal JP, Gresh N, Giessner-Prettre C. Improved formulas for the calculation of the electrostatic contribution to the intermolecular interaction energy from multipolar expansion of the electronic distribution Journal of Physical Chemistry A. 107: 10353-10359. DOI: 10.1021/jp035748t  1
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