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The dispersion interaction between a pair of parallel DNA double-helixstructures is investigated by means of the van der Waals density functional(vdW-DF) method. Each double-helix structure consists of an infinite repetitionof one B-DNA coil with 10 base pairs. This parameter-free density functionaltheory (DFT) study illustrates the initial step in a proposed vdW-DFcomputational strategy for large biomolecular problems. The strategy is tofirst perform a survey of interaction geometries, based on the evaluation ofthe van der Waals (vdW) attraction, and then limit the evaluation of theremaining DFT parts (specifically the expensive study of the kinetic-energyrepulsion) to the thus identified interesting geometries. Possibilities foraccelerating this second step is detailed in a separate study. For the B-DNAdimer, the variation in van der Waals attraction is explored at relativelyshort distances (although beyond the region of density overlap) for a 360degrees rotation. This study highlights the role of the structural motifs, likethe grooves, in enhancing or reducing the vdW interaction strength. We findthat to a first approximation, it is possible to compare the DNA double strandat large wall-to-wall separations to the cylindrical shape of a carbon nanotube(which is almost isotropic under rotation). We compare our first-principlesresults with the atom-based dispersive interaction predicted by DFT-D2 [J.Comp. Chem. 27, 1787 (2006)] and find agreement in the asymptotic region.However, we also find that the differences in the enhancement that occur atshorter distances reveal characteristic features that result from the fact thatthe vdW-DF method is an electron-based (as opposed to atom-based) description.

A van der Waals density functional mapping of attraction in DNA dimers