The Effect of Water Solvent on Theoretical NMR Spin – Spin Couplings in DNA: Improvement of Calculated Values by Application of Two Solvent Models


V. Sychrovský1, B. Schneider1, P. Hobza1, L. Žídek2, V. Sklenář2


1 J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, and Center for Complex Molecular Systems and Biomolecules, Dolejškova 3, 18223, Praha 8, Czech Republic

2 Laboratory of Biomolecular Structure and Dynamics and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37, Brno, Czech Republic


The NMR indirect spin – spin coupling constants calculated in DNA base pairs are compared with one–bond 1J(X,H), 1J(C,X) and two–bond 2J(X,H), (X=C,N) coupling constants measured in DNA hairpin molecule d(GCGAAGC) [1]. The two theoretical models of solvent: explicit and Polarized Continuum, were introduced. Both explicit and PCM solvent model provide a similar improvement of the calculated J constants when compared to the experimental data. The mean absolute deviation between the calculated and experimental couplings is significantly reduced by solvent inclusion, from 1.7 to 1.1 Hz for guanine, from 2.4 to 0.6 Hz for cytosine, and from 2.3 to 1.6 Hz for adenine. The strongest solvent shift was calculated for the 1J(C,H) coupling constants, particularly for the (C8,H8) coupling in guanine (6.1 Hz) and adenine, and the (C5,H5) and (C6,H6) couplings in cytosine. These changes in 1J(C,H) coupling seem to correspond to the charge transfer from water bonding and lone pair orbitals to the guanine anti-bonding C8-H8, C8-N7, and C8-N9 orbitals. From the close agreement between the calculated and experimental coupling constants we can deduce that the C-H group of the hairpin bases is extensively hydrated even when interaction with solvent is rather weak and non – specific.

[1] V. Sychrovský, B. Schneider, P. Hobza, L. Žídek, V. Sklenář, Physical Chemistry Chemical Physics, in press.