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Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions

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Department of Chemistry, Unilever Centre for Molecular Science Informatics, Lensfield Road, Cambridge CB2 1EW, U.K.
* To whom correspondence should be addressed. E-mail: [email protected]
Cite this: J. Chem. Inf. Model. 2009, 49, 4, 944–955
Publication Date (Web):March 23, 2009
Copyright © 2009 American Chemical Society

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    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.

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    100. Maximilian F. Koch, Sabrina Harteis, Iris D. Blank, Galina Pestel, Lutz F. Tietze, Christian Ochsenfeld, Sabine Schneider, Stephan A. Sieber. Structural, Biochemical, and Computational Studies Reveal the Mechanism of Selective Aldehyde Dehydrogenase 1A1 Inhibition by Cytotoxic Duocarmycin Analogues. Angewandte Chemie International Edition 2015, 54 (46) , 13550-13554.
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