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Issue 14, 2005
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How well can new-generation density functional methods describe stacking interactions in biological systems?

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Abstract

We compare the performance of four recently developed DFT methods (MPW1B95, MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods (B3LYP and B97-1) for the calculation of stacking interactions in six nucleic acid bases complexes and five amino acid pairs and for the calculation of hydrogen bonding interactions in two Watson–Crick type base pairs. We found that the four newly developed DFT methods give reasonable results for the stacking interactions in the DNA base pairs and amino acid pairs, whereas the previous DFT methods fail to describe interactions in these stacked complexes. We conclude that the new generation of DFT methods have greatly improved performance for stacking interaction as compared to previously available methods. We recommend the PWB6K method for investigating large DNA or protein systems where stacking plays an important role.

Graphical abstract: How well can new-generation density functional methods describe stacking interactions in biological systems?

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Publication details

The article was received on 18 May 2005, accepted on 31 May 2005 and first published on 09 Jun 2005


Article type: Communication
DOI: 10.1039/B507036H
Citation: Phys. Chem. Chem. Phys., 2005,7, 2701-2705
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    How well can new-generation density functional methods describe stacking interactions in biological systems?

    Y. Zhao and D. G. Truhlar, Phys. Chem. Chem. Phys., 2005, 7, 2701
    DOI: 10.1039/B507036H

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