New MP2 database of nucleic acid base trimers: How well reproduce DFT methods structure and binding energies?

Martin Kabeláč, Haydee Valdes, Edward C. Sherer, Chris Cramer, Pavel Hobza

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

A new database of nucleic acid base trimers has been developed that includes 141 geometries and stabilization energies obtained at the RI-MP2 level of theory with the TZVPP basis set. Compared to other databases, this one includes considerably more complicated structures; the various intermolecular interactions in the trimers are quite heterogeneous and in particular include simultaneous hydrogen bonding and stacking interactions, which is similar to the situation in real biomolecules. Validation against these benchmark data is therefore a more demanding task for approximate models, since correct descriptions of all energy terms is unlikely to be accomplished by fortuitous cancellations of systematic errors. The density functionals TPSS (both with and without an empirical dispersion term), PWB6K, M05-2X, and BH&H, and the self-consistent charge density functional tight binding method augmented with an empirical dispersion term (SCC-DFTB-D) were assessed for their abilities to accurately compute structures and energies. The best reproduction of the BSSE corrected RI-MP2 stabilization energies was achieved by the TPSS functional (TZVPP basis set) combined with empirical dispersion; removal of the dispersion correction leads to significantly degraded performance. The M05-2X and PWB6K functionals performed very well in reproducing the RI-MP2 geometries, but showed a systematic moderate underestimation of the magnitude of base stacking interactions. The SCC-DFTB-D method predicts geometries in fair agreement with RI-MP2; given its computational efficiency it represents a good option for initial scanning of potential energy surfaces of biopolymers. BH&H gives geometries of comparable quality to the other functionals but significantly overestimates interaction energies other than stacking. The whole database of geometries and interaction energies of the complexes can be found on the web page: http://www.rsc.org/suppdata/CP/b7/b707182e/index.sht.

Original languageEnglish (US)
Title of host publicationComputation in Modern Science and Engineering - Proceedings of the International Conference on Computational Methods in Science and Engineering 2007 (ICCMSE 2007)
Pages1244-1247
Number of pages4
Edition2
DOIs
StatePublished - Dec 1 2007
EventInternational Conference on Computational Methods in Science and Engineering 2007, ICCMSE 2007 - Corfu, Greece
Duration: Sep 25 2007Sep 30 2007

Publication series

NameAIP Conference Proceedings
Number2
Volume963
ISSN (Print)0094-243X
ISSN (Electronic)1551-7616

Other

OtherInternational Conference on Computational Methods in Science and Engineering 2007, ICCMSE 2007
CountryGreece
CityCorfu
Period9/25/079/30/07

Keywords

  • Ab initio
  • DFT
  • Database
  • Nucleic acid bases
  • Trimers

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