Predicting noncovalent interactions between aromatic biomolecules with London-dispersion-corrected DFT
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.
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ABSTRACT: Our previous benchmark CCSD(T)/ complete basis set limit calculations were collected into a database named begdb - Benchmark Energy and Geometry DataBase. Web-based interface to this database was prepared and is available at www.begdb.com. Users can browse, search and plot the data online or download structures and energy tables.Collection of Czechoslovak Chemical Communications 01/2008; 73:1261-1270. DOI:10.1135/cccc20081261
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ABSTRACT: London dispersion forces are of primordial importance in chemical and biological systems. The Kohn-Sham formalism of density functional theory combined with many popular approximated exchange-correlation functionals either provides sporadic results or fails completely to account for these forces. Dispersion-corrected atom-centered potentials mimic the effect of these forces via atomic orbital-dependent nonlocal potentials whose parameters are obtained by calibrating against references of chosen accuracy. This scheme has shown encouraging outcomes despite its empiricism; the aim of this communication is to give a brief review on the development and applications to date of this promising approach.CHIMIA International Journal for Chemistry 03/2008; 62(4):231-234. DOI:10.2533/chimia.2008.231
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ABSTRACT: This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature. We further extensively discuss methods that are available for base-stacking studies, complexity of comparison of stacking calculations with gas phase experiments, balance of forces in stacked complexes of nucleic acid bases, and the relation between QM and force field descriptions. We also review all recent calculations on base-stacking systems, including details analysis of the B-DNA stacking. Specific attention is paid to the highest accuracy QM calculations, to the decomposition of the interactions, and development of dispersion-balanced DFT methods. Future prospects of computational studies of base stacking are discussed.Physical Chemistry Chemical Physics 06/2008; 10(19):2595-610. DOI:10.1039/b719370j