Intermolecular magnetic interactions in stacked DNA base pairs

Abstract

The influence of pi-stacking on the magnetic properties of atoms that belong to adenine-thymine and guanine-cytosine pairs in sequences of three and five layers of DNA base pairs was analysed. As probes we used NMR spectroscopic parameters, which are among the most useful tools to learn about the transmission of magnetic interactions in molecules. Four DFT functionals were employed: B3LYP, BHANDLYP, KT2 and KT3, together with the SOPPA method. Besides, given that the number of non-hydrogen atoms of the supramolecular systems studied here is larger than 50 we applied a locally dense basis set scheme. Our results show that the piling up of a few Watson-Crick base pairs above and below a given pair modifies its NMR spectroscopic parameters by an amount that may be measurable and the percentage of variation does not depend on dispersion. We found that magnetic shieldings are more sensitive than J-couplings, and also that some atoms are more sensitive than others. Stacking affects the shielding of non-hydrogen atoms like nitrogens, that are donors in hydrogen bonds, HBs, and the carbons bonded to them. The amount of variation of these shieldings was found to be from 2% to 5% when the pairs are considered first as isolated, and then, placed in the middle of a sequence of three layers of base pairs. Such a variation becomes vanishingly small when the sequence contains more than three layers, showing that the stacking effect on NMR spectroscopic parameters has a local nature. We have also found a pattern for shieldings. First, equivalent atoms of similar monomers (thymine and adenine, or guanine and cytosine) have similar values of absolute shieldings in isolated pairs, and the amount of variation from isolated pairs to aggregates of a few pairs is also similar, meaning that equivalent atoms are affected in a similar manner by pi-stacking. Second, the hydrogen atoms which belong to hydrogen bonds are more sensitive to the piling up than the non-hydrogen atoms.

Nuclear Spin–Spin Couplings: Efficient Evaluation of Exact Exchange and Extension to Local Hybrid Functionals

“…An obvious complement to this feature is the idea of so-called “locally dense basis sets” (LDBSs), that is, the combination of larger basis sets for the atom/region of interest and smaller ones for the remainder of the molecule, as for SSCTs, only the electronic structure of the coupling atoms and their immediate vicinity matters. This concept was first employed in the calculation of chemical shifts. ,− It has been applied to SSCCs as well, mainly using the second order polarization propagator approximation. − Although LDBS have been used with DFT methods, , little investigation on the reliability of such a method has been done …”

“…61−64 Although LDBS have been used with DFT methods, 65,66 little investigation on the reliability of such a method has been done. 67 We have investigated the LDBS scheme on 15 molecules: adamantane, Al , naphthalene, and OF 2 . For these compounds in particular, it is not always clear which nuclei to include into a chemically meaningful surrounding of the coupling atoms as this would require a priori knowledge of the system.…”

Solvent effects on the NMR shieldings of stacked DNA base pairs

“…In previous work we studied the likely existence of the long-range transmission of intra-molecular interactions in small fragments of molecules of DNA that could influence the behavior of response properties. 15 To check this hypothesis we applied a simple theoretical model that included only the π-stacking and guanine–cytosine HB effects on the NMR shielding. We considered the shielding of atoms that belong to the central dimer of a Watson–Crick chain as a special sensor of the influence of those interactions.…”

“…The calculation of NMR parameters has contributed significantly to the understanding of molecular interactions involving bases of DNA and RNA. 14 As discussed in a previous publication, 15 stacking a few Watson–Crick base pairs above and below a given base pair modifies its NMR spectroscopic parameters by an experimentally measurable amount (results from vacuum studies). However, in addition to a suitable level of theory, the reliable calculation of NMR parameters requires the inclusion of solvent effects.…”