List of works - Jean-Philip Piquemal

A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations

scientific article published on 24 June 2016

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?

scientific article published on 12 July 2017

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

scientific article published in August 2014

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

scientific article published on 13 February 2018

AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms.

scientific article published on 9 April 2018

AMOEBA+ Classical Potential for Modeling Molecular Interactions

scientific article published on 11 June 2019

An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems

scientific article published on 26 January 2022

An optimized charge penetration model for use with the AMOEBA force field.

scientific article

Assessment of SAPT and Supermolecular EDA Approaches for the Development of Separable and Polarizable Force Fields

scientific article published on 21 April 2021

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

scientific article published on 21 April 2015

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

scientific article published on 2 June 2017

Capturing Many-Body Interactions with Classical Dipole Induction Models

scientific article

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

scientific article published on 31 March 2017

Characterizing Molecular Interactions in Chemical Systems

scientific article published in December 2014

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

scientific article published on 4 October 2016

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

scientific article published on 01 November 2014

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

scientific article published on 29 April 2021

Could the "Janus-like" properties of the halobenzene CX bond (X=Cl, Br) be leveraged to enhance molecular recognition?

scientific article published on 18 November 2014

DFT-steric-based energy decomposition analysis of intermolecular interactions

article

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

scientific article published on 16 May 2022

Elucidating the Phosphate Binding Mode of Phosphate-Binding Protein: The Critical Effect of Buffer Solution.

scientific article published on 11 June 2018

Entasis through hook-and-loop fastening in a glycoligand with cumulative weak forces stabilizing Cu(I).

scientific article published on 17 January 2015

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

scientific article published on 3 March 2014

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

scientific article

High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

scientific article published on 02 February 2021

Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding.

scientific article published on 31 July 2017

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

scientific article published on 9 October 2014

Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential

scientific article published on 30 December 2019

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

scientific article published on 26 March 2021

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

scientific article published on September 28, 2010

Importance of explicit smeared lone-pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange-repulsion and charge transfer contributions.

scientific article published on 30 May 2017

LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields.

scientific article published on 18 January 2016

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

scientific article published on 17 May 2019

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

scientific article published on January 2, 2012

Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field

scientific article

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

scientific article published on 29 May 2019

Molecular Dynamics Using Nonvariational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation, and Application to the Bond Capacity Model

scientific article published on 11 October 2019

New Way for Probing Bond Strength

scientific article published on 21 February 2020

O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

scientific article published on 08 February 2022

Open source variational quantum eigensolver extension of the quantum learning machine for quantum chemistry

scientific article published in 2023

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

scientific article published on July 13, 2010

Polarizable molecular dynamics in a polarizable continuum solvent

scientific article published on 26 January 2015

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

scientific article published on 11 September 2014

Preface: Special Topic: From Quantum Mechanics to Force Fields

scientific article

Pushing the Limits of Multiple-Time-Step Strategies for Polarizable Point Dipole Molecular Dynamics

scientific article published on 07 May 2019

QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential

scientific article published on 23 May 2018

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

scientific article published on 27 February 2014

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

scientific article published on 24 December 2014

Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations

scientific article published on 30 March 2020

Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle mesh Ewald.

scientific article published on June 2015

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

scientific article published on February 2016

Solvation effects drive the selectivity in Diels-Alder reaction under hyperbaric conditions

scientific article published on 20 May 2020

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

scientific article published on 20 July 2015

The Independent Gradient Model: A New Approach for Probing Strong and Weak Interactions in Molecules from Wave Function Calculations.

scientific article

The inhibition process of HIV-1 integrase by diketoacids molecules: Understanding the factors governing the better efficiency of dolutegravir.

scientific article published on 3 May 2017

The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces

scientific article

Tinker 8: Software Tools for Molecular Design

scientific article published on 19 September 2018

Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems

scientific article published on 23 March 2021

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

scientific article

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

scientific article published on 10 June 2017

Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings

scientific article published on 11 June 2019

Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations

scientific article published on 08 December 2016

Velocity jump processes: An alternative to multi-timestep methods for faster and accurate molecular dynamics simulations

scientific article published on 01 July 2020

List of works by Jean-Philip Piquemal

A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations

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?

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

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms.

AMOEBA+ Classical Potential for Modeling Molecular Interactions

An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems

An optimized charge penetration model for use with the AMOEBA force field.

Assessment of SAPT and Supermolecular EDA Approaches for the Development of Separable and Polarizable Force Fields

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

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

Capturing Many-Body Interactions with Classical Dipole Induction Models

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

Characterizing Molecular Interactions in Chemical Systems

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

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

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

Could the "Janus-like" properties of the halobenzene CX bond (X=Cl, Br) be leveraged to enhance molecular recognition?

DFT-steric-based energy decomposition analysis of intermolecular interactions

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

Elucidating the Phosphate Binding Mode of Phosphate-Binding Protein: The Critical Effect of Buffer Solution.

Entasis through hook-and-loop fastening in a glycoligand with cumulative weak forces stabilizing Cu(I).

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

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

High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding.

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

Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

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

Importance of explicit smeared lone-pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange-repulsion and charge transfer contributions.

LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields.

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

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

Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field

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

Molecular Dynamics Using Nonvariational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation, and Application to the Bond Capacity Model

New Way for Probing Bond Strength

O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

Open source variational quantum eigensolver extension of the quantum learning machine for quantum chemistry

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

Polarizable molecular dynamics in a polarizable continuum solvent

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

Preface: Special Topic: From Quantum Mechanics to Force Fields

Pushing the Limits of Multiple-Time-Step Strategies for Polarizable Point Dipole Molecular Dynamics

QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential

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

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

Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations

Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle mesh Ewald.

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

Solvation effects drive the selectivity in Diels-Alder reaction under hyperbaric conditions

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

The Independent Gradient Model: A New Approach for Probing Strong and Weak Interactions in Molecules from Wave Function Calculations.

The inhibition process of HIV-1 integrase by diketoacids molecules: Understanding the factors governing the better efficiency of dolutegravir.

The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces

Tinker 8: Software Tools for Molecular Design

Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

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

Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings

Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations

Velocity jump processes: An alternative to multi-timestep methods for faster and accurate molecular dynamics simulations