Volume 5 Supplement 1
Rationalisation and visualisation of non-bonded interactions
© Maginn et al.; licensee BioMed Central Ltd. 2013
Published: 22 March 2013
Models of non-bonded interactions are crucial in structure-based drug design. "Standard" hydrogen bonds are well modelled through traditional molecular mechanics forcefields with their treatments of electrostatics, and functional forms, often based on abundant crystal structure data, to describe their geometries. But "non-standard" interactions - for example, hydrogen bonds with carbon as the donor, or so-called halogen interactions - are not well handled, or not handled at all.
Here, we describe the use of extended Hückel (E-Hückel) theory, a very fast, low-level MO theory, to evaluate the geometries and energies of such non-standard interactions. These include successful modelling of halogen interactions for Cl, Br and I, which each display the so-called "sigma hole" in QM calculations, and likewise interactions between sulphur and oxygen. The E-Hückel modelling has been implemented in the 2011.10 version of the MOE (Molecular Operating Environment) software system.
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.