The dispersion interaction between a pair of parallel DNA double-helix structures is investigated by means of the van der Waals density functional (vdW-DF) method. Each double-helix structure consists of an infinite repetition of one B-DNA coil with
10 base pairs. This parameter-free density functional theory (DFT) study illustrates the initial step in a proposed vdW-DF computational strategy for large biomolecular problems. The strategy is to first perform a survey of interaction geometries, based on the evaluation of the van der Waals (vdW) attraction, and then limit the evaluation of the remaining DFT parts (specifically the expensive study of the kinetic-energy repulsion) to the thus identified interesting geometries. Possibilities for accelerating this second step is detailed in a separate study. For the B-DNA dimer, the variation in van der Waals attraction is explored at relatively short distances (although beyond the region of density overlap) for a 360 degrees rotation. This study highlights the role of the structural motifs, like the grooves, in enhancing or reducing the vdW interaction strength. We find that to a first approximation, it is possible to compare the DNA double strand at large wall-to-wall separations to the cylindrical shape of a carbon nanotube (which is almost isotropic under rotation). We compare our first-principles results 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 at shorter distances reveal characteristic features that result from the fact that the vdW-DF method is an electron-based (as opposed to atom-based) description.
Large biomolecular systems, whose function may involve thousands of atoms, cannot easily be addressed with parameter-free density functional theory (DFT) calculations. Until recently a central problem was that such systems possess an inherent sparsen
ess, that is, they are formed from components that are mutually separated by low-electron-density regions where dispersive forces contribute significantly to the cohesion and behavior. The introduction of, for example, the van der Waals density functional (vdW-DF) method [PRL 92, 246401 (2004)] has addressed part of this sparse-matter system challenge. However, while a vdW-DF study is often as computationally efficient as a study performed in the generalized gradient approximation, the scope of large-sparse-matter DFT is still limited by computer time and memory. It is costly to self-consistently determine the electron wavefunctions and hence the kinetic-energy repulsion. In this paper we propose and evaluate an adaption of the Harris scheme [PRB 31, 1770 (1985)]. This is done to speed up non-selfconsistent vdW-DF studies of molecular-system interaction energies. Also, the Harris-type analysis establishes a formal link between dispersion-interaction effects on the effective potential for electron dynamics and the impact of including selfconsistency in vdW-DF calculations [PRB 76, 125112 (2007)].
The past few years has brought renewed focus on the physics behind the class of materials characterized by long-range interactions and wide regions of low electron density, sparse matter. There is now much work on developing the appropriate algorithm
s and codes able to correctly describe this class of materials within a parameter-free quantum physical description. In particular, van der Waals (vdW) forces play a major role in building up material cohesion in sparse matter. This work presents an application to the vanadium pentoxide (V2O5) bulk structure of t
Sparse matter is characterized by regions with low electron density and its understanding calls for methods to accurately calculate both the van der Waals (vdW) interactions and other bonding. Here we present a first-principles density functional the
ory (DFT) study of a layered oxide (V2O5) bulk structure which shows charge voids in between the layers and we highlight the role of the vdW forces in building up material cohesion. The result of previous first-principles studies involving semilocal approximations to the exchange-correlation functional in DFT gave results in good agreement with experiments for the two in-plane lattice parameters of the unit cell but overestimated the parameter for the stacking direction. To recover the third parameter we include the nonlocal (dispersive) vdW interactions through the vdW-DF method [Dion et al., Phys. Rev. Lett. 92, 246401 (2004)] testing also various choices of exchange flavors. We find that the transferable first-principle vdW-DF calculations stabilizes the bulk structure. The vdW-DF method gives results in fairly good agreement with experiments for all three lattice parameters.
