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Issue 38, 2013
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Error estimates for (semi-)empirical dispersion terms and large biomacromolecules

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Abstract

The first-principles modeling of biomaterials has made tremendous advances over the last few years with the ongoing growth of computing power and impressive developments in the application of density functional theory (DFT) codes to large systems. One important step forward was the development of dispersion corrections for DFT methods, which account for the otherwise neglected dispersive van der Waals (vdW) interactions. Approaches at different levels of theory exist, with the most often used (semi-)empirical ones based on pair-wise interatomic C6R−6 terms. Similar terms are now also used in connection with semiempirical QM (SQM) methods and density functional tight binding methods (SCC-DFTB). Their basic structure equals the attractive term in Lennard-Jones potentials, common to most force field approaches, but they usually use some type of cutoff function to make the mixing of the (long-range) dispersion term with the already existing (short-range) dispersion and exchange-repulsion effects from the electronic structure theory methods possible. All these dispersion approximations were found to perform accurately for smaller systems, but error estimates for larger systems are very rare and completely missing for really large biomolecules. We derive such estimates for the dispersion terms of DFT, SQM and MM methods using error statistics for smaller systems and dispersion contribution estimates for the PDBbind database of proteinligand interactions. We find that dispersion terms will usually not be a limiting factor for reaching chemical accuracy, though some force fields and large ligand sizes are problematic.

Graphical abstract: Error estimates for (semi-)empirical dispersion terms and large biomacromolecules

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Publication details

The article was received on 25 Jun 2013, accepted on 31 Jul 2013 and first published on 01 Aug 2013


Article type: Paper
DOI: 10.1039/C3OB41309H
Citation: Org. Biomol. Chem., 2013,11, 6515-6519
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    Error estimates for (semi-)empirical dispersion terms and large biomacromolecules

    M. Korth, Org. Biomol. Chem., 2013, 11, 6515
    DOI: 10.1039/C3OB41309H

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