A stepwise phase-transfer extraction process improves the quality of electrophoretically-fractionated chiral Au-38(SG)(24) nanoclusters in water, as revealed by both absorption and CD spectroscopy. The effect of thiolate ligand structures on the CD response is then discussed. In the purified Au-38 nanocluster compound, simultaneous deconvolution analysis of both the absorption and CD spectra makes the unresolved transitions clear.