Determination of the 3D structure (configuration and preferred conformation) of complex natural and synthetic organic molecules is a long-standing but still challenging task for chemists, with various implications in pharmaceutical sciences whether or not these substances have specific bioactivities. NMR in aligning media, either lyotropic liquid crystals (LLC) or polymer gels, in combination with molecular modelling is a unique framework to solve complex structural problems whose analytical wealth lies in the establishment of non-local structural correlations. As an alternative to already well-established anisotropic NMR parameters, such as RDCs (residual dipolar couplings) and RCSAs (residual chemical shift anisotropies), it is shown here that deuterium residual quadrupolar couplings ( 2 H-RQCs) can be extracted from 2 H 2D-NMR spectra recorded at natural abundance level in samples oriented in a homopolypeptide LLC (PBLG). These 2 H-RQCs were successfully used to address non-trivial structural problems in organic molecules. The performance and scope of this new tool is examined for two natural chiral compounds of pharmaceutical interest (strychnine and artemisinin). This is the first report in which the 3D structure/relative configuration of complex bioactive molecules is unambiguously determined using only 2 H-RQCs, being in this case at 2 H natural abundance.