The pyramidalizations of N9/1 glycosidic nitrogens in DNA and RNA nucleosides, recently discovered and analyzed in their ultrahigh-resolution X-ray crystal structures (Sychrovsky; 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 3J(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 degrees to +25 degrees and from -5.7 degrees to +2.0 degrees, 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.