Evaluating the Effects of the Nonplanarity of Nucleic Acid Bases on NMR, IR, and Vibrational Circular Dichroism Spectra: A Density Functional Theory Computational Study

Abstract

The pyramidalizations of N9/1 glycosidic nitrogens in DNA and RNA nucleosides, recently discovered and analyzed in their ultrahigh-resolution X-ray crystal structures et al. Nucleic Acid Res. 2009, 37, 7321.), were found to have significant effects on the structural interpretation of the 3 J(C4/2-H1′) and 3 J(C8/ 6-H1′) NMR scalar couplings in purine/pyrimidine nucleosides. The calculated effects on IR and vibrational circular dichroism (VCD) spectra were only minor. The calculated structural deformations in nucleosides, depending on sugar-to-base orientation, gave rise to corrections in the phase shift of the Karplus equations for the 3 J(C8/6-H1′) and 3 J(C4/2-H1′) couplings ranging from -26°to +25°and from -5.7°to +2.0°, respectively. The sign alternation of this correction in syn and anti nucleosides arises from the stereoinversion of the N9/1 glycosidic nitrogen occurring upon reorientation of the glycosidic torsion. The effect was calculated consistently in the dG, dA, dC, dT, rA, and rG nucleosides. Utilization of the calculated phase-shift corrections in the design of Karplus equations for the 3 J couplings was suggested, and the effects on structural interpretation of the experimental couplings were evaluated.

Possible interactions between fused pyrazole derivative and magnesium ions - NMR experiments and theoretical calculations

“…We reasoned then that 1 H NMR is the most suitable technique for investigation of such interactions between azoles and metal ions. 24,25,[29][30][31] The NMR measurements were carried out at three different temperatures, namely at 25, 40 and 60 °C. The shifts in the signal positions refer to the experiments involving separately compound 7 and the same molecule in the presence of magnesium hydrate.…”

“…Usually, such small changes are omitted in this type of publications. 24,25,30,31 The pH alterations, even small, should be considered if the molecule contains easily ionisable groups or for compounds of specific physicochemical properties (amino acids, proteins). They are unimportant for small molecules that, like compound 7, contain practically one protonation site.…”