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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
Chapter
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 21)

Abstract

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.

Keywords

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.

Abbreviations

AMOEBA

Atomic multipoles optimized energetics for biological applications

APMM

Anisotropic polarizable molecular mechanics

ATP

Adenosine triphosphate

aug-cc-pVTZ

Augmented correlation-consistent polarized valence triple dzeta

BO

Born-Oppenheimer

CDP

Claverie, Dreyfus, Pullman

CEP

Coreless effective potential

CP

Car-Parrinello

CSOV

Constrained space orbital variation

CTU

Carboxythiourea

dd-Cosmo

Domain-decomposition conductor screening model

DIIS

Direct inversion of iterative space

EFP

Effective fragment potential

ELF

Electron localization function

EM

Energy-minimization

EVG

Elvitegravir

FAK

Focal adhesion kinase

FEP

Free energy perturbation

GEM

Gaussian electrostatic model

GPU

Graphics processor unit

GS

Garmer and Stevens

HF

Hartree-Fock

IEHT

Iterative extended Huckel theory

I-NoLLS

Interactive non linear least squares

INT

Integrase

KM

Kitaura-Morokuma

LC

Langlet-Claverie

LMO

Localized molecular orbitals

MC

Monte-Carlo

MD

Molecular dynamics

MEP

Molecular electrostatic potential

MO

Molecular orbitals

NA

Nucleic acids

NRP1

Neuropilin-1

OPEP

Optimized partitioning of electrostatic properties

PBC

Periodic boundary conditions

PME

Particle Mesh Ewald

PMI

Phosphomannose isomerase

PMM

Polarizable molecular mechanics

QC

Quantum chemistry

QM/MM

Quantum mechanics/molecular mechanics

RVS

Reduced variational space

SAPT

Symmetry-adapted perturbation theory

SIBFA

Sum of interactions between fragments Ab initio computed

SOD

Superoxide dismutase

vdW

van der Waals

Notes

Acknowledgments

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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