On the reliability of the AMBER force field and its empirical dispersion contribution for the description of noncovalent complexes

Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry
Michal KolárPavel Hobza

Abstract

The reliability of the AMBER force field is tested by comparing the total interaction energy and dispersion energy with the reference data obtained at the density functional theory-symmetry-adapted perturbation treatment (DFT-SAPT)/aug-cc-pVDZ level. The comparison is made for 194 different geometries of noncovalent complexes (H-bonded, stacked, mixed, and dispersion-bound), at the equilibrium distances as well as at longer distances (up to a relative distance of two). The total interaction energies agree very well with the reference data and only the strength of H-bonded complexes is slightly underestimated. In the case of dispersion energy, the overall agreement is even better, with the exception of the stacked aromatic systems, where the empirical dispersion energy is overestimated. The use of AMBER interaction energy and AMBER dispersion energy for different types of noncovalent complexes at equilibrium as well as at longer distances is thus justified, except for a few cases, such as the water molecule, where the dispersion energy is highly inaccurate.

References

Mar 28, 1992·Lancet·R Winter
Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
Feb 7, 2006·Journal of Molecular Graphics & Modelling·Junmei WangDavid A Case
Nov 4, 2008·Journal of the American Chemical Society·Jirí CernýPavel Hobza
Mar 25, 2009·Journal of Chemical Information and Modeling·Robert S Paton, Jonathan M Goodman
May 16, 2009·The Journal of Physical Chemistry. B·Jirí CernýPavel Hobza
Aug 21, 2009·The Journal of Chemical Physics·Laszlo Fusti MolnarKenneth M Merz
Dec 22, 2009·Physical Chemistry Chemical Physics : PCCP·Per-Olof Westlund, Håkan Wennerström
Jan 13, 2010·Physical Chemistry Chemical Physics : PCCP·Chen Wang, Stephen J Paddison
Feb 11, 2010·Physical Chemistry Chemical Physics : PCCP·R M Lynden-Bell
Jul 14, 2010·Chemistry : a European Journal·Kristine A NolinF Dean Toste

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Citations

Oct 1, 2011·The Journal of Physical Chemistry. a·Dimas SuárezHaydée Valdés
Sep 18, 2013·Proceedings of the National Academy of Sciences of the United States of America·Alan A Chen, Angel E García
Feb 5, 2013·Biochimica Et Biophysica Acta·Jarosław Poznański, David Shugar
Sep 20, 2011·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Rajesh K RajuSteven E Wheeler
Mar 14, 2012·Journal of Computational Chemistry·Ivo CacelliGiacomo Prampolini
Oct 6, 2016·Wiley Interdisciplinary Reviews. RNA·Sweta VangavetiAlan A Chen
Jul 9, 2017·Journal of Computer-aided Molecular Design·Wiktoria JedwabnyW Andrzej Sokalski
Jun 27, 2019·Physical Chemistry Chemical Physics : PCCP·Hugues LambertTung-Chun Lee
Sep 26, 2013·ACS Chemical Biology·Jason G HarrisonDean J Tantillo
Mar 13, 2015·The Journal of Physical Chemistry. B·Stefano PianaDavid E Shaw
Jun 12, 2012·Journal of Chemical Theory and Computation·Justin SpiritiArjan van der Vaart
Apr 10, 2012·Journal of Chemical Theory and Computation·Michal Kolář, Pavel Hobza
Nov 1, 2012·Journal of Chemical Theory and Computation·Aleksandar SpasicDavid H Mathews
May 18, 2011·The Journal of Physical Chemistry. B·Michal KolářPavel Hobza
Jun 14, 2011·Journal of Chemical Theory and Computation·Maxim Tafipolsky, Bernd Engels

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