Literature DB >> 19309094

Hydrogen bonding and pi-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions.

Robert S Paton1, Jonathan M Goodman.   

Abstract

We have evaluated the performance of a set of widely used force fields by calculating the geometries and stabilization energies for a large collection of intermolecular complexes. These complexes are representative of a range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Benchmark energies are taken from the high-level ab initio values in the JSCH-2005 and S22 data sets. All of the force fields underestimate stabilization resulting from hydrogen bonding, but the energetics of electrostatic and van der Waals interactions are described more accurately. OPLSAA gave a mean unsigned error of 2 kcal mol(-1) for all 165 complexes studied, and outperforms DFT calculations employing very large basis sets for the S22 complexes. The magnitude of hydrogen bonding interactions are severely underestimated by all of the force fields tested, which contributes significantly to the overall mean error; if complexes which are predominantly bound by hydrogen bonding interactions are discounted, the mean unsigned error of OPLSAA is reduced to 1 kcal mol(-1). For added clarity, web-based interactive displays of the results have been developed which allow comparisons of force field and ab initio geometries to be performed and the structures viewed and rotated in three dimensions.

Entities:  

Mesh:

Year:  2009        PMID: 19309094     DOI: 10.1021/ci900009f

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  31 in total

1.  Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields.

Authors:  Hari S Muddana; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2012-01-25       Impact factor: 3.686

2.  Driving torsion scans with wavefront propagation.

Authors:  Yudong Qiu; Daniel G A Smith; Chaya D Stern; Mudong Feng; Hyesu Jang; Lee-Ping Wang
Journal:  J Chem Phys       Date:  2020-06-28       Impact factor: 3.488

3.  Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.

Authors:  Hari S Muddana; C Daniel Varnado; Christopher W Bielawski; Adam R Urbach; Lyle Isaacs; Matthew T Geballe; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2012-02-25       Impact factor: 3.686

4.  Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: a molecular dynamics study of cellobiose stereoisomers.

Authors:  Dongqi Wang; Maria Lovísa Ámundadóttir; Wilfred F van Gunsteren; Philippe H Hünenberger
Journal:  Eur Biophys J       Date:  2013-05-10       Impact factor: 1.733

5.  Calculating the sensitivity and robustness of binding free energy calculations to force field parameters.

Authors:  Gabriel J Rocklin; David L Mobley; Ken A Dill
Journal:  J Chem Theory Comput       Date:  2013-07-09       Impact factor: 6.006

6.  Hydrogen-Bond-Dependent Conformational Switching: A Computational Challenge from Experimental Thermochemistry.

Authors:  James Luccarelli; Robert S Paton
Journal:  J Org Chem       Date:  2019-01-09       Impact factor: 4.354

7.  Performance of four different force fields for simulations of dipeptide conformations: GlyGly, GlyGly-, GlyGly · Cl-, GlyGly · Na+ and GlyGly · (H2O)2.

Authors:  Chen Dong; Li Yong-Zhi; Wei Zhi-Chao; Liu Bo
Journal:  J Mol Model       Date:  2014-05-27       Impact factor: 1.810

8.  Computational Study on the Conformations of Mitragynine and Mitragynaline.

Authors:  Haining Liu; Christopher R McCurdy; Robert J Doerksen
Journal:  Theochem       Date:  2010-04-15

9.  Transition State Force Field for the Asymmetric Redox-Relay Heck Reaction.

Authors:  Anthony R Rosales; Sean P Ross; Paul Helquist; Per-Ola Norrby; Matthew S Sigman; Olaf Wiest
Journal:  J Am Chem Soc       Date:  2020-05-14       Impact factor: 15.419

10.  Locating a plausible binding site for an open-channel blocker, GlyH-101, in the pore of the cystic fibrosis transmembrane conductance regulator.

Authors:  Yohei Norimatsu; Anthony Ivetac; Christopher Alexander; Nicolette O'Donnell; Leah Frye; Mark S P Sansom; David C Dawson
Journal:  Mol Pharmacol       Date:  2012-08-24       Impact factor: 4.436

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.