Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Accurate Interaction Energies of Base Pairing and Base Stacking. The Final Chapter

Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. We present new reference ab initio structures and interaction energies of selected base pairs with binding energies ranging from -5 to -47 kcal/mol. The molecular structures are obtained using the RI-MP2 (resolution of identity MP2) method with extended cc-pVTZ basis set of atomic orbitals. The RI-MP2 method provides results essentially identical with the standard MP2 method. The interaction energies are calculated using the Complete Basis Set (CBS) extrapolation at the RI-MP2 level. For some base pairs Coupled-Cluster corrections with inclusion of noniterative triple contributions (CCSD(T)) are given. The calculations are compared with selected medium quality methods. The PW91 DFT functional with the 6-31G** basis set matches well the RI-MP2/CBS absolute interaction energies and reproduces the relative values of base pairing energies with a maximum relative error of 2.6 kcal/mol when applied with Becke3LYP-optimized geometries. The Becke3LYP DFT functional underestimates the interaction energies by few kcal/mol with relative error of 2.2 kcal/mol. Very good performance of non-polarizable Cornell et al. (AMBER) force field is confirmed. This indirectly supports the view that H-bonded base pairs are primarily stabilized by electrostatic interactions. Similar systematic calculations for base stacking are under way, all with inclusion of the key triple electron excitations, and the results will be presented. After two decades of ab initio research, the present numbers converged to provide close to ultimate predictions of intrinsic energetics of H-bonding and stacking of NA bases. The overall agreement with the preceding reference studies reported by us in the middle of nineties is rather satisfactory and only small corrections are expected due to future improvements of QM theory.

References and Footnotes
  1. Sponer, J., Jurecka, P., and Hobza, P. J. Am. Chem. Soc. 126, 10142-10151 (2004).
  2. Jurecka, P., Sponer, J., and Hobza, P. J. Phys. Chem. B 108, 5466-5471 (2004).
  3. Hobza, P. and Sponer, J. Chem. Rev. 99, 3247-3276 (1999).

Jiri Sponer1,2,*
Petr Jurecka2
Pavel Hobza2,*

1Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
612 65 Brno, Czech Republic
2Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Flemingovo nam. 2
166 10 Prague, Czech Republic

*Corresponding authors:
Institute of Biophysics
Fax: 420 5412 12179
Email: sponer@ncbr.chemi.muni.cz
Institute of Organic Chemistry and Biochemistry
Email: pavel.hobza@uochb.cas.cz