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Issue 16, 2008
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OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application

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Abstract

The semiempirical methods of the OMx family (orthogonalization models OM1, OM2, and OM3) are known to describe biochemical systems more accurately than standard semiempirical approaches such as AM1. We investigate the benefits of augmenting these methods with an empirical dispersion term (OMx-D) taken from recent density functional work, without modifying the standard OMx parameters. Significant improvements are achieved for non-covalent interactions, with mean unsigned errors of 1.41 kcal/mol (OM2-D) and 1.31 kcal/mol (OM3-D) for the binding energy of the complexes in the JSCH-2005 data base. This supports the use of these augmented methods in quantum mechanical/molecular mechanical (QM/MM) studies of biomolecules, for example during system preparation and equilibration. As an illustrative application, we present QM and QM/MM calculations on the binding between antibody 34E4 and a hapten, where OM3-D performs better than the methods without dispersion terms (AM1, OM3).

Graphical abstract: OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application

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Supplementary files

Article information


Submitted
05 Dec 2007
Accepted
25 Jan 2008
First published
25 Feb 2008

Phys. Chem. Chem. Phys., 2008,10, 2159-2166
Article type
Paper

OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application

T. Tuttle and W. Thiel, Phys. Chem. Chem. Phys., 2008, 10, 2159
DOI: 10.1039/B718795E

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