Predicting Noncovalent Interactions between Aromatic Biomolecules with London-Dispersion-Corrected DFT

ArticleinThe Journal of Physical Chemistry B 111(51):14346-54 · December 2007with10 Reads
DOI: 10.1021/jp0750102 · Source: PubMed
Abstract
Within the framework of Kohn-Sham density functional theory, interaction energies of hydrogen bonded and pi-pi stacked supramolecular complexes of aromatic heterocycles, nucleobase pairs, and complexes of nucleobases with the anti-cancer agent ellipticine as well as its derivatives are evaluated. Dispersion-corrected atom-centered potentials (DCACPs) are employed together with a generalized gradient approximation to the exchange correlation functional. For all systems presented, the DCACP calculations are in very good agreement with available post Hartree-Fock quantum chemical results. Estimates of 3-body contributions (<15% of the respective interaction energy) and deformation energies (5-15% of the interaction energy) are given. Based on our results, we predict a strongly bound interaction energy profile for the ellipticine intercalation process with a stabilization of nearly 40 kcal/mol (deformation energy not taken into account) when fully intercalated. The frontier orbitals of the intercalator-nucleobase complex and the corresponding non-intercalated nucleobases are investigated and show significant changes upon intercalation. The results not only offer some insights into the systems investigated but also suggest that DCACPs can serve as an effective way to achieve higher accuracy in density functional theory without incurring an unaffordable computational overhead, paving ways for more realistic studies on biomolecular complexes in the condensed phase.
    • "First, we calculated the interaction energy for two Watson-Crick-bound DNA base pairs, connected through charged sugar-phosphate backbone, into which ellipticine is intercalated (Fig 8 (a)). The binding energy was estimated to amount to ≈ 37 kcal/mol from a dispersion-corrected DFT method,[67] 48 kcal/mol from the Tkatchenko-Scheffler method (i.e., without subsequent SCS),[16] 50.7 kcal/mol from the non-rangeseparated MBD method with DFT,[23] and 33.6 ± 0.9 kcal/mol from diffusion quantum Monte Carlo. [68] The complex has significant π-π stacking and manybody effects.[16] "
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