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 Lagardère
  • Filippo Lipparini
  • Jean-Philip Piquemal
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 21)


We review two essential features of the intermolecular interaction energies (ΔE) computed in the context of quantum chemistry (QC): non-isotropy and non-additivity. Energy-decomposition analyses show the extent to which each comes into play in the separate ΔE contributions, namely electrostatic, short-range repulsion, polarization, charge-transfer and dispersion. Such contributions have their counterparts in anisotropic, polarizable molecular mechanics (APMM), and each of these should display the same features as in QC. We review examples to evaluate the performances of APMM in this respect. They bear on the complexes of one or several ligands with metal cations, and on multiply H-bonded complexes. We also comment on the involvement of polarization, a key contributor to non-additivity, in the issues of multipole transferability and conjugation. In the last section we provide recent examples of APMM validations by QC, which relate to interactions taking place in the recognition sites of kinases and metalloproteins. We conclude by mentioning prospects of extensive applications of APMM.


Quantum Chemistry Focal Adhesion Kinase Molecular Electrostatic Potential Water Network Polarization Energy 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



Atomic multipoles optimized energetics for biological applications


Anisotropic polarizable molecular mechanics


Adenosine triphosphate


Augmented correlation-consistent polarized valence triple dzeta




Claverie, Dreyfus, Pullman


Coreless effective potential




Constrained space orbital variation




Domain-decomposition conductor screening model


Direct inversion of iterative space


Effective fragment potential


Electron localization function






Focal adhesion kinase


Free energy perturbation


Gaussian electrostatic model


Graphics processor unit


Garmer and Stevens




Iterative extended Huckel theory


Interactive non linear least squares








Localized molecular orbitals




Molecular dynamics


Molecular electrostatic potential


Molecular orbitals


Nucleic acids




Optimized partitioning of electrostatic properties


Periodic boundary conditions


Particle Mesh Ewald


Phosphomannose isomerase


Polarizable molecular mechanics


Quantum chemistry


Quantum mechanics/molecular mechanics


Reduced variational space


Symmetry-adapted perturbation theory


Sum of interactions between fragments Ab initio computed


Superoxide dismutase


van der Waals



We wish to thank Dr. Michael Devereux (University of Basel, Switzerland) for his recent contributions on Pb(II) modeling, and for enabling to derive INollS-optimized SIBFA parameters in conjunction with the aug-cc-pVTZ(-f) basis set. Several colleagues are thanked for rewarding collaborations in the last few years: Tom Darden (Open Eyes, Santa Fe, USA), G. Andres Cisneros (University of Detroit, USA), Aude Marjolin (Quantum Theory Project, Pittsburgh, USA), Marie Ledecq (Union Chimiques Belges, Brussels, Belgium), Johan Wouters (Universites Notre-Dame de la Paix, Namur, Belgium), Dr. Dorothée Berthomieu (Dorothée Berthomieu, Institut Charles-Gerhardt, Université de Montpellier, France) and Markus Meuwly (University of Basel, Switzerland). We would also like to mention, regarding the experimental work, Prof. Christiane Garbay (Université ParisDescartes, Paris, France) and Prof. Laurent Salmon (Institut de Chimie Moléculaire d’Orsay, France).

We wish to thank the Grand Equipement National de Calcul Intensif (GENCI): Institut du Développement et des Ressources en Informatique Scientifique (IDRIS), Centre Informatique de l’Enseignement Supérieur (CINES), France, project No. x2009-075009), and the Centre de Ressources Informatiques de Haute Normandie (CRIHAN, Rouen, France), project 1998053. This work was supported in part by the French state funds managed by CALSIMLAB and the ANR within the Investissements d’Avenir program under reference ANR-11-IDEX-0004-02. F.L. We also wish to thank the Association Philippe Jabre (Beirut, Lebanon) for financing the PhD Thesis of Krystel El Hage.


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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Nohad Gresh
    • 1
    • 2
  • Krystel El Hage
    • 1
    • 3
  • Elodie Goldwaser
    • 1
    • 2
  • Benoit de Courcy
    • 1
    • 2
  • Robin Chaudret
    • 2
  • David Perahia
    • 4
  • Christophe Narth
    • 2
  • Louis Lagardère
    • 2
  • Filippo Lipparini
    • 2
  • Jean-Philip Piquemal
    • 2
  1. 1.Chemistry and Biology Nucleo(S)Tides and Immunology for Therapy (CBNIT)UMR 8601 CNRS, UFR BiomédicaleParisFrance
  2. 2.Laboratoire de Chimie ThéoriqueSorbonne Universités, UPMC, UMR7616 CNRSParisFrance
  3. 3.Faculté des SciencesCentre d’Analyses et de Recherche, UR EGFEM, Saint Joseph University of BeirutBeirutLebanon
  4. 4.Laboratoire de Biologie et de Pharmacologie Appliquées (LPBA)UMR 8113 CNRS, Ecole Normale Supérieure de CachanParisFrance

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