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Addressing the Issues of Non-isotropy and Non-additivity in the Development of Quantum Chemistry-Grounded Polarizable Molecular Mechanics

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Quantum Modeling of Complex Molecular Systems

Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((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.

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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

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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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  1. Krystel El Hage

    Present address: Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland

Authors and Affiliations

  1. Chemistry and Biology Nucleo(S)Tides and Immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomédicale, Paris, France

    Nohad Gresh, Krystel El Hage, Elodie Goldwaser & Benoit de Courcy

  2. Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, UMR7616 CNRS, Paris, France

    Nohad Gresh, Elodie Goldwaser, Benoit de Courcy, Robin Chaudret, Christophe Narth, Louis Lagardère, Filippo Lipparini & Jean-Philip Piquemal

  3. Faculté des Sciences, Centre d’Analyses et de Recherche, UR EGFEM, Saint Joseph University of Beirut, Beirut, 1107 2050, Lebanon

    Krystel El Hage

  4. Laboratoire de Biologie et de Pharmacologie Appliquées (LPBA), UMR 8113 CNRS, Ecole Normale Supérieure de Cachan, Paris, France

    David Perahia

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  1. Nohad Gresh
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Correspondence to Nohad Gresh .

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  1. UMR 7565—SRSMC, Université de Lorraine, Nancy-Vandoeuvre, France

    Jean-Louis Rivail

  2. UMR 7565—SRSMC, Université de Lorraine, Nancy-Vandoeuvre, France

    Manuel Ruiz-Lopez

  3. UMR 7565—SRSMC, Université de Lorraine, Nancy-Vandoeuvre, France

    Xavier Assfeld

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Gresh, N. et al. (2015). Addressing the Issues of Non-isotropy and Non-additivity in the Development of Quantum Chemistry-Grounded Polarizable Molecular Mechanics. In: Rivail, JL., Ruiz-Lopez, M., Assfeld, X. (eds) Quantum Modeling of Complex Molecular Systems. Challenges and Advances in Computational Chemistry and Physics, vol 21. Springer, Cham. https://doi.org/10.1007/978-3-319-21626-3_1

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