Predicting noncovalent interactions between aromatic biomolecules with London-dispersion-corrected DFT.
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.
Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
I-Chun
IC
Lin
O Anatole von
OA
Lilienfeld
Maurício D
MD
Coutinho-Neto
Ivano
I
Tavernelli
Ursula
U
Rothlisberger
D000465:Algorithms; D000970:Antineoplastic Agents / Q000737:chemistry*; D020029:Base Pairing; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011237:Predictive Value of Tests; D011687:Purines / Q000737:chemistry*; D011743:Pyrimidines / Q000737:chemistry*; D011789:Quantum Theory; D013816:Thermodynamics
D000970:Antineoplastic Agents; D011687:Purines; D011743:Pyrimidines