Literature DB >> 19093829

How accurate can a force field become? A polarizable multipole model combined with fragment-wise quantum-mechanical calculations.

Pär Söderhjelm1, Ulf Ryde.   

Abstract

A new method to accurately estimate the interaction energy between a large molecule and a smaller ligand is presented. The method approximates the electrostatic and induction contributions classically by multipole and polarizability expansions, but uses explicit quantum-mechanical fragment calculations for the remaining (nonclassical) contributions, mainly dispersion and exchange repulsion. Thus, it represents a limit of how accurate a force field can ever become for interaction energies if pairwise additivity of the nonclassical term is assumed (e.g., all general-purpose force fields). The accuracy is tested by considering protein-ligand model systems for which the true MP2/6-31G* interaction energies can be computed. The method is shown to be more accurate than related fragmentation approaches. The remaining error (2-5 and approximately10 kJ/mol for neutral and charged ligands, respectively) can be decreased by including the polarizing effect from surrounding fragments in the quantum-mechanical calculations.

Mesh:

Year:  2009        PMID: 19093829     DOI: 10.1021/jp8073514

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.781


  13 in total

1.  The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

Authors:  Yue Shi; Zhen Xia; Jiajing Zhang; Robert Best; Chuanjie Wu; Jay W Ponder; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2013       Impact factor: 6.006

2.  Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies.

Authors:  Paulius Mikulskis; Daniela Cioloboc; Milica Andrejić; Sakshi Khare; Joakim Brorsson; Samuel Genheden; Ricardo A Mata; Pär Söderhjelm; Ulf Ryde
Journal:  J Comput Aided Mol Des       Date:  2014-04-04       Impact factor: 3.686

3.  Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model.

Authors:  Karen Oda Hjorth Minde Dundas; Maarten T P Beerepoot; Magnus Ringholm; Simen Reine; Radovan Bast; Nanna Holmgaard List; Jacob Kongsted; Kenneth Ruud; Jógvan Magnus Haugaard Olsen
Journal:  J Chem Theory Comput       Date:  2021-05-19       Impact factor: 6.006

Review 4.  The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.

Authors:  Samuel Genheden; Ulf Ryde
Journal:  Expert Opin Drug Discov       Date:  2015-04-02       Impact factor: 6.098

5.  Quantifying electron transfer reactions in biological systems: what interactions play the major role?

Authors:  Emil Sjulstok; Jógvan Magnus Haugaard Olsen; Ilia A Solov'yov
Journal:  Sci Rep       Date:  2015-12-22       Impact factor: 4.379

6.  How Far Does a Receptor Influence Vibrational Properties of an Odorant?

Authors:  Anna Reese; Nanna Holmgaard List; Jacob Kongsted; Ilia A Solov'yov
Journal:  PLoS One       Date:  2016-03-25       Impact factor: 3.240

7.  Combining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease.

Authors:  Prashant Kumar; Paulina Maria Dominiak
Journal:  Molecules       Date:  2021-06-24       Impact factor: 4.411

8.  The effective fragment molecular orbital method for fragments connected by covalent bonds.

Authors:  Casper Steinmann; Dmitri G Fedorov; Jan H Jensen
Journal:  PLoS One       Date:  2012-07-23       Impact factor: 3.240

9.  Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

Authors:  Martin A Olsson; Pär Söderhjelm; Ulf Ryde
Journal:  J Comput Chem       Date:  2016-04-27       Impact factor: 3.376

10.  Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T).

Authors:  Octav Caldararu; Martin A Olsson; Christoph Riplinger; Frank Neese; Ulf Ryde
Journal:  J Comput Aided Mol Des       Date:  2016-09-06       Impact factor: 3.686

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