All Stories

  1. How to make continuum solvation incredibly fast in a few simple steps: A practical guide to the domain decomposition paradigm for the conductor-like screening model

    Article • International Journal of Quantum Chemistry, August 2018, Wiley

    Professor Jean-Philip Piquemal

  2. Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

    Article • Journal of Computational Chemistry, June 2017, Wiley

    Professor Jean-Philip Piquemal

  3. Butanethiol adsorption and dissociation on Ag (111): A periodic DFT study

    Article • Surface Science, April 2016, Elsevier

    Professor Jean-Philip Piquemal

  4. Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles

    Article • Journal of Computational Chemistry, January 2016, Wiley

    Professor Jean-Philip Piquemal

  5. Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics.

    Article • The Journal of Physical Chemistry, July 2015, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  6. General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field

    Article • Journal of Chemical Theory and Computation, June 2015, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  7. Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Toward Massively Parallel Computations Using Smooth Particle Mesh Ewald

    Article • Journal of Chemical Theory and Computation, June 2015, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  8. Polarizable Force Fields for Biomolecular Modeling

    Article • May 2015, Wiley

    Professor Jean-Philip Piquemal

  9. Bridging organometallics and quantum chemical topology: Understanding electronic relocalisation during palladium-catalyzed reductive elimination

    Article • Journal of Computational Chemistry, April 2015, Wiley

    Professor Jean-Philip Piquemal

  10. Polarizable Molecular Dynamics in a Polarizable Continuum Solvent

    Article • Journal of Chemical Theory and Computation, February 2015, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  11. Entasis through Hook-and-Loop Fastening in a Glycoligand with Cumulative Weak Forces Stabilizing Cu I

    Article • Journal of the American Chemical Society, January 2015, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  12. Characterizing Molecular Interactions in Chemical Systems

    Article • IEEE Transactions on Visualization and Computer Graphics, December 2014, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Jean-Philip Piquemal

  13. Quantum-chemistry based calibration of the alkali metal cation series (Li+Cs+) for large-scale polarizable molecular mechanics/dynamics simulations

    Article • Journal of Computational Chemistry, December 2014, Wiley

    Professor Jean-Philip Piquemal

  14. Could the “Janus-like” properties of the halobenzene CX bond (XCl, Br) be leveraged to enhance molecular recognition?

    Article • Journal of Computational Chemistry, November 2014, Wiley

    Professor Jean-Philip Piquemal

  15. Quantum, classical, and hybrid QM/MM calculations in solution: General implementation of the ddCOSMO linear scaling strategy

    Article • The Journal of Chemical Physics, November 2014, American Institute of Physics

    Professor Jean-Philip Piquemal

  16. 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

    Article • Journal of Molecular Modeling, November 2014, Springer Science + Business Media

    Professor Jean-Philip Piquemal

  17. 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

    Article • The Journal of Physical Chemistry A, October 2014, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  18. Hydration gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics

    Article • Journal of Molecular Modeling, October 2014, Springer Science + Business Media

    Professor Jean-Philip Piquemal

  19. Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: Bimetallic binding site and structured waters

    Article • Journal of Computational Chemistry, September 2014, Wiley

    Professor Jean-Philip Piquemal

  20. 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

    Article • The Journal of Physical Chemistry A, September 2014, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

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

    Article • Bioorganic & Medicinal Chemistry Letters, September 2014, Elsevier

    Professor Jean-Philip Piquemal

  22. A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field

    Article • Journal of Computational Chemistry, June 2014, Wiley

    Professor Jean-Philip Piquemal

  23. Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field

    Article • The Journal of Physical Chemistry, June 2014, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  24. Revisiting H 2 O Nucleation around Au + and Hg 2+ : The Peculiar “Pseudo-Soft” Character of the Gold Cation

    Article • Journal of Chemical Theory and Computation, May 2014, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  25. DFT-steric-based energy decomposition analysis of intermolecular interactions

    Article • Theoretical Chemistry Accounts, April 2014, Springer Science + Business Media

    Professor Jean-Philip Piquemal

  26. GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations

    Article • Journal of Chemical Theory and Computation, April 2014, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

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

    Article • Journal of Chemical Theory and Computation, April 2014, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  28. Quantum Calculations in Solution for Large to Very Large Molecules: A New Linear Scaling QM/Continuum Approach

    Article • The Journal of Physical Chemistry Letters, March 2014, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  29. Understanding the structure and electronic properties of Th 4+ -water complexes

    Article • Canadian Journal of Chemistry, September 2013, Canadian Science Publishing

    Professor Jean-Philip Piquemal

  30. Further refinements of next-generation force fields — Nonempirical localization of off-centered points in molecules

    Article • Canadian Journal of Chemistry, September 2013, Canadian Science Publishing

    Professor Jean-Philip Piquemal

  31. Are Bond Critical Points Really Critical for Hydrogen Bonding?

    Article • Journal of Chemical Theory and Computation, August 2013, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  32. Understanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins

    Article • Journal of Chemical Theory and Computation, May 2013, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  33. Toward a Deeper Understanding of Enzyme Reactions Using the Coupled ELF/NCI Analysis: Application to DNA Repair Enzymes

    Article • Journal of Chemical Theory and Computation, May 2013, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  34. Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds?

    Article • Journal of Computational Chemistry, February 2013, Wiley

    Professor Jean-Philip Piquemal

  35. From Quantum Mechanics to Force Fields

    Article • January 2013

    Professor Jean-Philip Piquemal

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

    Article • Journal of Chemical Theory and Computation, November 2012, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  37. Ionic interactions: Comparative topological approach

    Article • Computational and Theoretical Chemistry, October 2012, Elsevier

    Professor Jean-Philip Piquemal

  38. Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential

    Article • Journal of Chemical Theory and Computation, April 2012, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  39. Toward a ligand specific of Pb2+ with respect to the Zn2+ and Ca2+ cations: A track from quantum chemistry

    Article • Chemical Physics Letters, April 2012, Elsevier

    Professor Jean-Philip Piquemal

  40. From quantum mechanics to force fields: new methodologies for the classical simulation of complex systems

    Article • March 2012, Springer Science + Business Media

    Professor Jean-Philip Piquemal

  41. From quantum mechanics to force fields: new methodologies for the classical simulation of complex systems

    Article • Theoretical Chemistry Accounts, March 2012, Springer Science + Business Media

    Professor Jean-Philip Piquemal

  42. Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies

    Article • March 2012, Springer Science + Business Media

    Professor Jean-Philip Piquemal

  43. Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies

    Article • Theoretical Chemistry Accounts, March 2012, Springer Science + Business Media

    Professor Jean-Philip Piquemal

  44. Competitive ligand/chelate binding in [Cu(TMPA)]+ and [Cu(tren)]+ based complexes

    Article • Catalysis Today, November 2011, Elsevier

    Professor Jean-Philip Piquemal

  45. Many-body exchange-repulsion in polarizable molecular mechanics. I. orbital-based approximations and applications to hydrated metal cation complexes

    Article • Journal of Computational Chemistry, July 2011, Wiley

    Professor Jean-Philip Piquemal

  46. Polarizable Water Networks in Ligand–Metalloprotein Recognition. Impact on the Relative Complexation Energies of Zn-Dependent Phosphomannose Isomerase with d -Mannose 6-Phosphate Surrogates

    Article • The Journal of Physical Chemistry, June 2011, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  47. NCIPLOT: A Program for Plotting Noncovalent Interaction Regions

    Article • Journal of Chemical Theory and Computation, March 2011, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  48. Electron Pair Localization Function (EPLF) for Density Functional Theory and ab Initio Wave Function-Based Methods: A New Tool for Chemical Interpretation

    Article • Journal of Chemical Theory and Computation, March 2011, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal, Michel Caffarel

  49. Unraveling Low-Barrier Hydrogen Bonds in Complex Systems with a Simple Quantum Topological Criterion

    Article • Chemistry - A European Journal, February 2011, Wiley

    Professor Jean-Philip Piquemal

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

    Article • Journal of Chemical Theory and Computation, January 2011, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  51. Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations

    Article • Physical Chemistry Chemical Physics, January 2011, Royal Society of Chemistry

    Professor Jean-Philip Piquemal

  52. Spin-driven activation of dioxygen in various metalloenzymes and their inspired models

    Article • Journal of Computational Chemistry, November 2010, Wiley

    Professor Jean-Philip Piquemal, Michel Caffarel

  53. The reaction mechanism of type I phosphomannose isomerases: New information from inhibition and polarizable molecular mechanics studies

    Article • Proteins Structure Function and Bioinformatics, November 2010, Wiley

    Professor Jean-Philip Piquemal

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

    Article • Journal of Chemical Theory and Computation, July 2010, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

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

    Article • International Journal of Quantum Chemistry, June 2010, Wiley

    Professor Jean-Philip Piquemal

  56. 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

    Article • The Journal of Physical Chemistry, April 2010, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  57. Polarizable Water Molecules in Ligand−Macromolecule Recognition. Impact on the Relative Affinities of Competing Pyrrolopyrimidine Inhibitors for FAK Kinase

    Article • Journal of the American Chemical Society, March 2010, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  58. Editorial: Special issue on quantum mechanical modeling of biological systems

    Article • Interdisciplinary Sciences Computational Life Sciences, January 2010, Springer Science + Business Media

    Professor Jean-Philip Piquemal

  59. Gaussian Multipole Model (GMM)

    Article • Journal of Chemical Theory and Computation, January 2010, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  60. 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

    Article • Bioorganic & Medicinal Chemistry, October 2009, Elsevier

    Professor Jean-Philip Piquemal

  61. Dioxygen Activation by Mononuclear Copper Enzymes: Insights from a Tripodal Ligand Mimicking Their Cu M Coordination Sphere

    Article • Inorganic Chemistry, August 2009, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  62. Fragment-Localized Kohn−Sham Orbitals via a Singles Configuration-Interaction Procedure and Application to Local Properties and Intermolecular Energy Decomposition Analysis†

    Article • Journal of Chemical Theory and Computation, December 2008, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  63. Energy Analysis of Zn Polycoordination in a Metalloprotein Environment and of the Role of a Neighboring Aromatic Residue. What Is the Impact of Polarization?

    Article • Journal of Chemical Theory and Computation, October 2008, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  64. Understanding Lead Chemistry from Topological Insights: The Transition between Holo- and Hemidirected Structures within the [Pb(CO)n]2+ Model Series

    Article • Chemistry - A European Journal, March 2008, Wiley

    Professor Jean-Philip Piquemal

  65. Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments

    Article • Journal of Computational Chemistry, January 2008, Wiley

    Professor Jean-Philip Piquemal

  66. Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand−Macromolecule Complexes. A Bottom-Up Strategy

    Article • Journal of Chemical Theory and Computation, November 2007, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  67. Numerical Fitting of Molecular Properties to Hermite Gaussians

    Article • The Journal of Physical Chemistry A, November 2007, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  68. Specificity of Acyl Transfer from 2-Mercaptobenzamide Thioesters to the HIV-1 Nucleocapsid Protein

    Article • Journal of the American Chemical Society, September 2007, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  69. Key Role of the Polarization Anisotropy of Water in Modeling Classical Polarizable Force Fields

    Article • The Journal of Physical Chemistry A, August 2007, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal, Dr piero procacci

  70. Toward a Separate Reproduction of the Contributions to the Hartree−Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential †

    Article • Journal of Chemical Theory and Computation, May 2007, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  71. Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase fromCandida albicans studied by polarizable molecular mechanics and quantum mechanics

    Article • Journal of Computational Chemistry, January 2007, Wiley

    Professor Jean-Philip Piquemal

  72. Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods

    Article • The Journal of Chemical Physics, November 2006, American Institute of Physics

    Professor Jean-Philip Piquemal

  73. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

    Article • The Journal of Chemical Physics, August 2006, American Institute of Physics

    Professor Jean-Philip Piquemal

  74. Quantum Mechanics/Molecular Mechanics Electrostatic Embedding with Continuous and Discrete Functions

    Article • The Journal of Physical Chemistry, July 2006, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  75. [Pb(H2O)]2+ and [Pb(OH)]+: Four-component density functional theory calculations, correlated scalar relativistic constrained-space orbital variation energy decompositions, and topological analysis

    Article • The Journal of Chemical Physics, May 2006, American Institute of Physics

    Professor Jean-Philip Piquemal

  76. Comments on the nature of the bonding in oxygenated dinuclear copper enzyme models

    Article • Journal of Molecular Structure THEOCHEM, May 2006, Elsevier

    Professor Jean-Philip Piquemal

  77. Towards a force field based on density fitting

    Article • The Journal of Chemical Physics, March 2006, American Institute of Physics

    Professor Jean-Philip Piquemal

  78. Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallelab initiocomputations

    Article • Journal of Computational Chemistry, August 2005, Wiley

    Professor Jean-Philip Piquemal

  79. Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-β-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry

    Article • Journal of Computational Chemistry, August 2005, Wiley

    Professor Jean-Philip Piquemal

  80. A CSOV study of the difference between HF and DFT intermolecular interaction energy values: The importance of the charge transfer contribution

    Article • Journal of Computational Chemistry, July 2005, Wiley

    Professor Jean-Philip Piquemal

  81. Intermolecular electrostatic energies using density fitting

    Article • The Journal of Chemical Physics, July 2005, American Institute of Physics

    Professor Jean-Philip Piquemal

  82. Revisiting the geometry of nd10 (n+1)s0 [M(H2O)]p+ complexes using four-component relativistic DFT calculations and scalar relativistic correlated CSOV energy decompositions (Mp+ = Cu+, Zn2+, Ag+, Cd2+, Au+, Hg2+)

    Article • Journal of Computational Chemistry, January 2005, Wiley

    Professor Jean-Philip Piquemal

  83. Improved Formulas for the Calculation of the Electrostatic Contribution to the Intermolecular Interaction Energy from Multipolar Expansion of the Electronic Distribution

    Article • The Journal of Physical Chemistry A, December 2003, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal

  84. Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF

    Article • Journal of Computational Chemistry, December 2003, Wiley

    Professor Jean-Philip Piquemal

  85. Theoretical study of phenol and 2-aminophenol docking at a model of the tyrosinase active site

    Article • New Journal of Chemistry, January 2003, Royal Society of Chemistry

    Professor Jean-Philip Piquemal

  86. Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF

    Article • Journal of Computational Chemistry, January 2003, Wiley

    Professor Jean-Philip Piquemal